#work_calculate_uni-multimappers-etc.md
Table of contents
Code: Get situated
#!/bin/bash
# tmux new -s htseq
# tmux a -t htseq
grabnode # 4, defaults
source activate gff3_env
ml SAMtools/1.16.1-GCC-11.2.0
transcriptome &&
{
cd "results/2023-0215/" \
|| echo "cd'ing failed; check on this..."
}
.,Code: Get situated
#!/bin/bash
for h in ./outfiles_htseq-count/already/combined-SC-KL-20S/U*; do
if [[ ! -e "${h}" ]]; then
mkdir -p outfiles_htseq-count
else
echo "Directories present; skipping mkdir'ing of outfile directories"
fi
break
doneCode: Set up arrays
#!/bin/bash
unset UT_prim_UMI
typeset -a UT_prim_UMI
while IFS=" " read -r -d $'\0'; do
UT_prim_UMI+=( "${REPLY}" )
done < <(\
find "bams_renamed/UT_prim_UMI" \
-type l \
-name "*.bam" \
-print0 \
| sort -z \
)
echo_test "${UT_prim_UMI[@]}"
echo "${#UT_prim_UMI[@]}"Code: Index all bams in arrays
#!/bin/bash
for h in ./bams_renamed/UT_prim_UMI/*.bai; do
if [[ ! -e "${h}" ]]; then
for i in "${UT_prim_UMI[@]}"; do
echo "Indexing ${i}"
samtools index -@ "${SLURM_CPUS_ON_NODE}" "${i}"
echo ""
done
else
echo "Bam indices exist; skipping the running of samtools index"
fi
break
doneCode: Collect metrics on unimappers, multimappers, etc.
#!/bin/bash
if [[ -f outfiles_htseq-count/calculate_uni-multimappers-etc.UT_prim_UMI.txt ]]; then
rm outfiles_htseq-count/calculate_uni-multimappers-etc.UT_prim_UMI.txt
fi
echo \
"sample"$'\t'"sample_total"$'\t'"Mito-KL-20S_all"$'\t'"Mito-KL-20S_uni"$'\t'"Mito-KL-20S_multi"$'\t'"SC-I-XVI_all"$'\t'"SC-I-XVI_uni"$'\t'"SC-I-XVI_multi" \
> outfiles_htseq-count/calculate_uni-multimappers-etc.UT_prim_UMI.txt
for i in "${UT_prim_UMI[@]}"; do
# i="${UT_prim_UMI[0]}" # echo "${i}"
# Get sample name
c_name="$(basename "${i}" ".UT_prim_UMI.bam")" # echo "${c_name}"
# Get total number of counts (read pairs) for sample
unset tmp
tmp="$(samtools view -c "${i}")" # echo "${tmp}"
c_all=$(( tmp / 2 )) # echo "${c_all}"
# Calculate number of unimappers for non-I-XIV chromosomes
unset tmp
tmp="$(
samtools view -@ "${SLURM_CPUS_ON_NODE}" \
"${i}" \
Mito A B C D E F 20S \
| awk '/\<NH:i:1\>/' \
| wc -l
)" # echo "${tmp}"
c_MK2_uni=$(( tmp / 2 )) # echo "${c_MK2_uni}"
# Calculate number of multimappers for non-I-XIV chromosomes
unset tmp
tmp="$(
samtools view -@ "${SLURM_CPUS_ON_NODE}" \
"${i}" \
Mito A B C D E F 20S \
| awk '!/\<NH:i:1\>/' \
| wc -l
)" # echo "${tmp}"
c_MK2_multi=$(( tmp / 2 )) # echo "${c_MK2_multi}"
# Get (and check) the sum of non-I-XIV chromosome counts
c_MK2_sum=$(( c_MK2_uni + c_MK2_multi )) # echo "${c_MK2_sum}"
c_MK2_sum_check="$(
samtools view -@ "${SLURM_CPUS_ON_NODE}" -c \
"${i}" \
Mito A B C D E F 20S
)" # echo "${c_MK2_sum_check}"
[[ $(( c_MK2_sum_check / 2 )) -eq c_MK2_sum ]] ||
{
echo "Values are not equal; check on this..."
return 1
}
# Calculate number of unimappers for I-XIV chromosomes
unset tmp
tmp="$(
samtools view -@ "${SLURM_CPUS_ON_NODE}" \
"${i}" \
I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI \
| awk '/\<NH:i:1\>/' \
| wc -l
)" # echo "${tmp}"
c_chr_uni=$(( tmp / 2 )) # echo "${c_chr_uni}"
# Calculate number of multimappers for I-XIV chromosomes
unset tmp
tmp="$(
samtools view -@ "${SLURM_CPUS_ON_NODE}" \
"${i}" \
I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI \
| awk '!/\<NH:i:1\>/' \
| wc -l
)" # echo "${tmp}"
c_chr_multi=$(( tmp / 2 )) # echo "${c_chr_multi}"
# Get (and check) the sum of I-XIV chromosome counts
c_chr_sum=$(( c_chr_uni + c_chr_multi )) # echo "${c_chr_sum}"
c_chr_sum_check="$(
samtools view -@ "${SLURM_CPUS_ON_NODE}" -c \
"${i}" \
I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI
)" # echo "${c_chr_sum_check}"
[[ $(( c_chr_sum_check / 2 )) -eq c_chr_sum ]] ||
{
echo "Values are not equal; check on this..."
return 1
}
echo "Writing to dataframe..."
echo " c_name ${c_name}"
echo " c_all ${c_all}"
echo " c_MK2_uni ${c_MK2_uni}"
echo " c_MK2_multi ${c_MK2_multi}"
echo " c_MK2_sum ${c_MK2_sum}"
echo "c_MK2_sum_check ${c_MK2_sum_check}"
echo " c_chr_uni ${c_chr_uni}"
echo " c_chr_multi ${c_chr_multi}"
echo " c_chr_sum ${c_chr_sum}"
echo "c_chr_sum_check ${c_chr_sum_check}"
echo ""
echo \
"${c_name}"$'\t'"${c_all}"$'\t'"${c_MK2_sum}"$'\t'"${c_MK2_uni}"$'\t'"${c_MK2_multi}"$'\t'"${c_chr_sum}"$'\t'"${c_chr_uni}"$'\t'"${c_chr_multi}" \
>> outfiles_htseq-count/calculate_uni-multimappers-etc.UT_prim_UMI.txt
done
cat outfiles_htseq-count/calculate_uni-multimappers-etc.UT_prim_UMI.txtPrinted: Collect metrics on unimappers, multimappers, etc.
❯ for i in "${UT_prim_UMI[@]}"; do
> # i="${UT_prim_UMI[0]}" # echo "${i}"
>
> # Get sample name
> c_name="$(basename "${i}" ".UT_prim_UMI.bam")" # echo "${c_name}"
>
> # Get total number of counts (read pairs) for sample
> unset tmp
> tmp="$(samtools view -c "${i}")" # echo "${tmp}"
> c_all=$(( tmp / 2 )) # echo "${c_all}"
>
> # Calculate number of unimappers for non-I-XIV chromosomes
> unset tmp
> tmp="$(
> samtools view -@ "${SLURM_CPUS_ON_NODE}" \
> "${i}" \
> Mito A B C D E F 20S \
> | awk '/\<NH:i:1\>/' \
> | wc -l
> )" # echo "${tmp}"
> c_MK2_uni=$(( tmp / 2 )) # echo "${c_MK2_uni}"
>
> # Calculate number of multimappers for non-I-XIV chromosomes
> unset tmp
> tmp="$(
> samtools view -@ "${SLURM_CPUS_ON_NODE}" \
> "${i}" \
> Mito A B C D E F 20S \
> | awk '!/\<NH:i:1\>/' \
> | wc -l
> )" # echo "${tmp}"
> c_MK2_multi=$(( tmp / 2 )) # echo "${c_MK2_multi}"
>
> # Get (and check) the sum of non-I-XIV chromosome counts
> c_MK2_sum=$(( c_MK2_uni + c_MK2_multi )) # echo "${c_MK2_sum}"
> c_MK2_sum_check="$(
> samtools view -@ "${SLURM_CPUS_ON_NODE}" -c \
> "${i}" \
> Mito A B C D E F 20S
> )" # echo "${c_MK2_sum_check}"
> [[ $(( c_MK2_sum_check / 2 )) -eq c_MK2_sum ]] ||
> {
> echo "Values are not equal; check on this..."
> return 1
> }
>
> # Calculate number of unimappers for I-XIV chromosomes
> unset tmp
> tmp="$(
> samtools view -@ "${SLURM_CPUS_ON_NODE}" \
> "${i}" \
> I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI \
> | awk '/\<NH:i:1\>/' \
> | wc -l
> )" # echo "${tmp}"
> c_chr_uni=$(( tmp / 2 )) # echo "${c_chr_uni}"
>
> # Calculate number of multimappers for I-XIV chromosomes
> unset tmp
> tmp="$(
> samtools view -@ "${SLURM_CPUS_ON_NODE}" \
> "${i}" \
> I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI \
> | awk '!/\<NH:i:1\>/' \
> | wc -l
> )" # echo "${tmp}"
> c_chr_multi=$(( tmp / 2 )) # echo "${c_chr_multi}"
>
> # Get (and check) the sum of I-XIV chromosome counts
> c_chr_sum=$(( c_chr_uni + c_chr_multi )) # echo "${c_chr_sum}"
> c_chr_sum_check="$(
> samtools view -@ "${SLURM_CPUS_ON_NODE}" -c \
> "${i}" \
> I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI
> )" # echo "${c_chr_sum_check}"
> [[ $(( c_chr_sum_check / 2 )) -eq c_chr_sum ]] ||
> {
> echo "Values are not equal; check on this..."
> return 1
> }
>
> echo "Writing to dataframe..."
> echo " c_name ${c_name}"
> echo " c_all ${c_all}"
> echo " c_MK2_uni ${c_MK2_uni}"
> echo " c_MK2_multi ${c_MK2_multi}"
> echo " c_MK2_sum ${c_MK2_sum}"
> echo "c_MK2_sum_check ${c_MK2_sum_check}"
> echo " c_chr_uni ${c_chr_uni}"
> echo " c_chr_multi ${c_chr_multi}"
> echo " c_chr_sum ${c_chr_sum}"
> echo "c_chr_sum_check ${c_chr_sum_check}"
> echo ""
>
> echo \
> "${c_name}"$'\t'"${c_all}"$'\t'"${c_MK2_sum}"$'\t'"${c_MK2_uni}"$'\t'"${c_MK2_multi}"$'\t'"${c_chr_sum}"$'\t'"${c_chr_uni}"$'\t'"${c_chr_multi}" \
> >> outfiles_htseq-count/calculate_uni-multimappers-etc.UT_prim_UMI.txt
> done
Writing to dataframe...
c_name n3-d_Q_day7_tcn_N_aux-T_tc-F_rep1_tech1
c_all 28593750
c_MK2_uni 13723802
c_MK2_multi 2116564
c_MK2_sum 15840366
c_MK2_sum_check 31680732
c_chr_uni 9618005
c_chr_multi 3135379
c_chr_sum 12753384
c_chr_sum_check 25506768
Writing to dataframe...
c_name n3-d_Q_day7_tcn_N_aux-T_tc-F_rep2_tech1
c_all 29274110
c_MK2_uni 15496048
c_MK2_multi 2628223
c_MK2_sum 18124271
c_MK2_sum_check 36248542
c_chr_uni 7740567
c_chr_multi 3409272
c_chr_sum 11149839
c_chr_sum_check 22299678
Writing to dataframe...
c_name n3-d_Q_day7_tcn_N_aux-T_tc-F_rep3_tech1
c_all 32294104
c_MK2_uni 14561827
c_MK2_multi 2808044
c_MK2_sum 17369871
c_MK2_sum_check 34739742
c_chr_uni 10839993
c_chr_multi 4084240
c_chr_sum 14924233
c_chr_sum_check 29848466
Writing to dataframe...
c_name n3-d_Q_day7_tcn_SS_aux-T_tc-F_rep1_tech1
c_all 29462906
c_MK2_uni 17008920
c_MK2_multi 1889446
c_MK2_sum 18898366
c_MK2_sum_check 37796732
c_chr_uni 5254921
c_chr_multi 5309619
c_chr_sum 10564540
c_chr_sum_check 21129080
Writing to dataframe...
c_name n3-d_Q_day7_tcn_SS_aux-T_tc-F_rep2_tech1
c_all 30485089
c_MK2_uni 18942478
c_MK2_multi 2022018
c_MK2_sum 20964496
c_MK2_sum_check 41928992
c_chr_uni 4284572
c_chr_multi 5236021
c_chr_sum 9520593
c_chr_sum_check 19041186
Writing to dataframe...
c_name n3-d_Q_day7_tcn_SS_aux-T_tc-F_rep3_tech1
c_all 24769078
c_MK2_uni 14275293
c_MK2_multi 1712857
c_MK2_sum 15988150
c_MK2_sum_check 31976300
c_chr_uni 4164893
c_chr_multi 4616035
c_chr_sum 8780928
c_chr_sum_check 17561856
Writing to dataframe...
c_name o-d_Q_day7_tcn_N_aux-T_tc-F_rep1_tech1
c_all 26199413
c_MK2_uni 14487580
c_MK2_multi 2574502
c_MK2_sum 17062082
c_MK2_sum_check 34124164
c_chr_uni 5897639
c_chr_multi 3239692
c_chr_sum 9137331
c_chr_sum_check 18274662
Writing to dataframe...
c_name o-d_Q_day7_tcn_N_aux-T_tc-F_rep2_tech1
c_all 25614430
c_MK2_uni 15243591
c_MK2_multi 2613757
c_MK2_sum 17857348
c_MK2_sum_check 35714696
c_chr_uni 4329477
c_chr_multi 3427605
c_chr_sum 7757082
c_chr_sum_check 15514164
Writing to dataframe...
c_name o-d_Q_day7_tcn_SS_aux-T_tc-F_rep1_tech1
c_all 27546890
c_MK2_uni 11997347
c_MK2_multi 3331932
c_MK2_sum 15329279
c_MK2_sum_check 30658558
c_chr_uni 3428982
c_chr_multi 8788629
c_chr_sum 12217611
c_chr_sum_check 24435222
Writing to dataframe...
c_name o-d_Q_day7_tcn_SS_aux-T_tc-F_rep2_tech1
c_all 27650067
c_MK2_uni 13663469
c_MK2_multi 2765487
c_MK2_sum 16428956
c_MK2_sum_check 32857912
c_chr_uni 3564552
c_chr_multi 7656559
c_chr_sum 11221111
c_chr_sum_check 22442222
Writing to dataframe...
c_name r1-n_Q_day8_tcn_N_aux-F_tc-F_rep1_tech1
c_all 26074381
c_MK2_uni 10085027
c_MK2_multi 1957967
c_MK2_sum 12042994
c_MK2_sum_check 24085988
c_chr_uni 10241422
c_chr_multi 3789965
c_chr_sum 14031387
c_chr_sum_check 28062774
Writing to dataframe...
c_name r1-n_Q_day8_tcn_N_aux-F_tc-F_rep2_tech1
c_all 27859800
c_MK2_uni 10797819
c_MK2_multi 2237951
c_MK2_sum 13035770
c_MK2_sum_check 26071540
c_chr_uni 10653110
c_chr_multi 4170920
c_chr_sum 14824030
c_chr_sum_check 29648060
Writing to dataframe...
c_name r1-n_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1
c_all 28872243
c_MK2_uni 16807216
c_MK2_multi 2337439
c_MK2_sum 19144655
c_MK2_sum_check 38289310
c_chr_uni 3483824
c_chr_multi 6243764
c_chr_sum 9727588
c_chr_sum_check 19455176
Writing to dataframe...
c_name r1-n_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1
c_all 26452129
c_MK2_uni 16482900
c_MK2_multi 1935679
c_MK2_sum 18418579
c_MK2_sum_check 36837158
c_chr_uni 2959398
c_chr_multi 5074152
c_chr_sum 8033550
c_chr_sum_check 16067100
Writing to dataframe...
c_name r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1
c_all 14862518
c_MK2_uni 1751924
c_MK2_multi 2030973
c_MK2_sum 3782897
c_MK2_sum_check 7565794
c_chr_uni 7189320
c_chr_multi 3890301
c_chr_sum 11079621
c_chr_sum_check 22159242
Writing to dataframe...
c_name r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1
c_all 18842139
c_MK2_uni 2040193
c_MK2_multi 2471007
c_MK2_sum 4511200
c_MK2_sum_check 9022400
c_chr_uni 9406289
c_chr_multi 4924650
c_chr_sum 14330939
c_chr_sum_check 28661878
Writing to dataframe...
c_name r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1
c_all 14693909
c_MK2_uni 3677835
c_MK2_multi 2704814
c_MK2_sum 6382649
c_MK2_sum_check 12765298
c_chr_uni 4644448
c_chr_multi 3666812
c_chr_sum 8311260
c_chr_sum_check 16622520
Writing to dataframe...
c_name r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1
c_all 17701239
c_MK2_uni 4535393
c_MK2_multi 3011644
c_MK2_sum 7547037
c_MK2_sum_check 15094074
c_chr_uni 6119775
c_chr_multi 4034427
c_chr_sum 10154202
c_chr_sum_check 20308404
Writing to dataframe...
c_name r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1
c_all 17676487
c_MK2_uni 2748189
c_MK2_multi 2810627
c_MK2_sum 5558816
c_MK2_sum_check 11117632
c_chr_uni 7713092
c_chr_multi 4404579
c_chr_sum 12117671
c_chr_sum_check 24235342
Writing to dataframe...
c_name r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1
c_all 18673410
c_MK2_uni 2774145
c_MK2_multi 2951215
c_MK2_sum 5725360
c_MK2_sum_check 11450720
c_chr_uni 8210263
c_chr_multi 4737787
c_chr_sum 12948050
c_chr_sum_check 25896100
Writing to dataframe...
c_name r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1
c_all 20109413
c_MK2_uni 8170752
c_MK2_multi 3805030
c_MK2_sum 11975782
c_MK2_sum_check 23951564
c_chr_uni 3853707
c_chr_multi 4279924
c_chr_sum 8133631
c_chr_sum_check 16267262
Writing to dataframe...
c_name r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1
c_all 27172906
c_MK2_uni 7306541
c_MK2_multi 7449306
c_MK2_sum 14755847
c_MK2_sum_check 29511694
c_chr_uni 3856299
c_chr_multi 8560760
c_chr_sum 12417059
c_chr_sum_check 24834118
Writing to dataframe...
c_name r6-n_G1_day1_tcn_SS_aux-F_tc-F_rep1_tech1
c_all 26649217
c_MK2_uni 2288830
c_MK2_multi 4437167
c_MK2_sum 6725997
c_MK2_sum_check 13451994
c_chr_uni 10633162
c_chr_multi 9290058
c_chr_sum 19923220
c_chr_sum_check 39846440
Writing to dataframe...
c_name r6-n_G1_day1_tcn_SS_aux-F_tc-F_rep2_tech1
c_all 26995608
c_MK2_uni 2223334
c_MK2_multi 4088070
c_MK2_sum 6311404
c_MK2_sum_check 12622808
c_chr_uni 11425076
c_chr_multi 9259128
c_chr_sum 20684204
c_chr_sum_check 41368408
Writing to dataframe...
c_name r6-n_Q_day8_tcn_N_aux-F_tc-F_rep1_tech1
c_all 28279689
c_MK2_uni 9184377
c_MK2_multi 1925200
c_MK2_sum 11109577
c_MK2_sum_check 22219154
c_chr_uni 13364739
c_chr_multi 3805373
c_chr_sum 17170112
c_chr_sum_check 34340224
Writing to dataframe...
c_name r6-n_Q_day8_tcn_N_aux-F_tc-F_rep2_tech1
c_all 27494489
c_MK2_uni 10814101
c_MK2_multi 2067684
c_MK2_sum 12881785
c_MK2_sum_check 25763570
c_chr_uni 10933792
c_chr_multi 3678912
c_chr_sum 14612704
c_chr_sum_check 29225408
Writing to dataframe...
c_name r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1
c_all 37273438
c_MK2_uni 14994726
c_MK2_multi 4637440
c_MK2_sum 19632166
c_MK2_sum_check 39264332
c_chr_uni 3932961
c_chr_multi 13708311
c_chr_sum 17641272
c_chr_sum_check 35282544
Writing to dataframe...
c_name r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech2
c_all 31127425
c_MK2_uni 12492174
c_MK2_multi 3876582
c_MK2_sum 16368756
c_MK2_sum_check 32737512
c_chr_uni 3226890
c_chr_multi 11531779
c_chr_sum 14758669
c_chr_sum_check 29517338
Writing to dataframe...
c_name r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1
c_all 29051610
c_MK2_uni 16215412
c_MK2_multi 2377581
c_MK2_sum 18592993
c_MK2_sum_check 37185986
c_chr_uni 4427289
c_chr_multi 6031328
c_chr_sum 10458617
c_chr_sum_check 20917234
Writing to dataframe...
c_name t4-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1
c_all 18639826
c_MK2_uni 1538212
c_MK2_multi 2614833
c_MK2_sum 4153045
c_MK2_sum_check 8306090
c_chr_uni 8938957
c_chr_multi 5547824
c_chr_sum 14486781
c_chr_sum_check 28973562
Writing to dataframe...
c_name t4-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1
c_all 17426630
c_MK2_uni 1326048
c_MK2_multi 2385541
c_MK2_sum 3711589
c_MK2_sum_check 7423178
c_chr_uni 8391340
c_chr_multi 5323701
c_chr_sum 13715041
c_chr_sum_check 27430082
Writing to dataframe...
c_name t4-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1
c_all 19276505
c_MK2_uni 5191638
c_MK2_multi 3463960
c_MK2_sum 8655598
c_MK2_sum_check 17311196
c_chr_uni 6151066
c_chr_multi 4469841
c_chr_sum 10620907
c_chr_sum_check 21241814
Writing to dataframe...
c_name t4-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1
c_all 19092950
c_MK2_uni 5445342
c_MK2_multi 3303184
c_MK2_sum 8748526
c_MK2_sum_check 17497052
c_chr_uni 6102549
c_chr_multi 4241875
c_chr_sum 10344424
c_chr_sum_check 20688848
Writing to dataframe...
c_name t4-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1
c_all 20391336
c_MK2_uni 2240497
c_MK2_multi 3286534
c_MK2_sum 5527031
c_MK2_sum_check 11054062
c_chr_uni 8515633
c_chr_multi 6348672
c_chr_sum 14864305
c_chr_sum_check 29728610
Writing to dataframe...
c_name t4-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1
c_all 20894588
c_MK2_uni 2541675
c_MK2_multi 3351411
c_MK2_sum 5893086
c_MK2_sum_check 11786172
c_chr_uni 9126826
c_chr_multi 5874676
c_chr_sum 15001502
c_chr_sum_check 30003004
Writing to dataframe...
c_name t4-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1
c_all 17788422
c_MK2_uni 7287411
c_MK2_multi 3310517
c_MK2_sum 10597928
c_MK2_sum_check 21195856
c_chr_uni 3628475
c_chr_multi 3562019
c_chr_sum 7190494
c_chr_sum_check 14380988
Writing to dataframe...
c_name t4-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1
c_all 19014451
c_MK2_uni 8176542
c_MK2_multi 3560371
c_MK2_sum 11736913
c_MK2_sum_check 23473826
c_chr_uni 3533077
c_chr_multi 3744461
c_chr_sum 7277538
c_chr_sum_check 14555076
Writing to dataframe...
c_name WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1
c_all 17528651
c_MK2_uni 1291305
c_MK2_multi 2025142
c_MK2_sum 3316447
c_MK2_sum_check 6632894
c_chr_uni 9170938
c_chr_multi 5041266
c_chr_sum 14212204
c_chr_sum_check 28424408
Writing to dataframe...
c_name WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1
c_all 14354209
c_MK2_uni 1025775
c_MK2_multi 1828444
c_MK2_sum 2854219
c_MK2_sum_check 5708438
c_chr_uni 6997554
c_chr_multi 4502436
c_chr_sum 11499990
c_chr_sum_check 22999980
Writing to dataframe...
c_name WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1
c_all 17870971
c_MK2_uni 4821046
c_MK2_multi 3748328
c_MK2_sum 8569374
c_MK2_sum_check 17138748
c_chr_uni 4704206
c_chr_multi 4597391
c_chr_sum 9301597
c_chr_sum_check 18603194
Writing to dataframe...
c_name WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1
c_all 18187692
c_MK2_uni 4874871
c_MK2_multi 3593595
c_MK2_sum 8468466
c_MK2_sum_check 16936932
c_chr_uni 5105886
c_chr_multi 4613340
c_chr_sum 9719226
c_chr_sum_check 19438452
Writing to dataframe...
c_name WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1
c_all 16268286
c_MK2_uni 2069852
c_MK2_multi 2594807
c_MK2_sum 4664659
c_MK2_sum_check 9329318
c_chr_uni 6924408
c_chr_multi 4679219
c_chr_sum 11603627
c_chr_sum_check 23207254
Writing to dataframe...
c_name WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1
c_all 18162697
c_MK2_uni 2144943
c_MK2_multi 3056330
c_MK2_sum 5201273
c_MK2_sum_check 10402546
c_chr_uni 7185078
c_chr_multi 5776346
c_chr_sum 12961424
c_chr_sum_check 25922848
Writing to dataframe...
c_name WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1
c_all 18353221
c_MK2_uni 7388417
c_MK2_multi 3934090
c_MK2_sum 11322507
c_MK2_sum_check 22645014
c_chr_uni 2984238
c_chr_multi 4046476
c_chr_sum 7030714
c_chr_sum_check 14061428
Writing to dataframe...
c_name WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech2
c_all 29105695
c_MK2_uni 8020750
c_MK2_multi 8496223
c_MK2_sum 16516973
c_MK2_sum_check 33033946
c_chr_uni 3374316
c_chr_multi 9214406
c_chr_sum 12588722
c_chr_sum_check 25177444
Writing to dataframe...
c_name WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1
c_all 16959938
c_MK2_uni 7036884
c_MK2_multi 3351052
c_MK2_sum 10387936
c_MK2_sum_check 20775872
c_chr_uni 2789045
c_chr_multi 3782957
c_chr_sum 6572002
c_chr_sum_check 13144004
Writing to dataframe...
c_name WT_G1_day1_ovn_N_aux-F_tc-F_rep1_tech1
c_all 15634566
c_MK2_uni 353542
c_MK2_multi 61849
c_MK2_sum 415391
c_MK2_sum_check 830782
c_chr_uni 13188385
c_chr_multi 2030790
c_chr_sum 15219175
c_chr_sum_check 30438350
Writing to dataframe...
c_name WT_G1_day1_ovn_N_aux-F_tc-F_rep2_tech1
c_all 15755143
c_MK2_uni 625995
c_MK2_multi 75139
c_MK2_sum 701134
c_MK2_sum_check 1402268
c_chr_uni 12953728
c_chr_multi 2100281
c_chr_sum 15054009
c_chr_sum_check 30108018
Writing to dataframe...
c_name WT_G1_day1_ovn_SS_aux-F_tc-F_rep1_tech1
c_all 10723500
c_MK2_uni 753929
c_MK2_multi 570797
c_MK2_sum 1324726
c_MK2_sum_check 2649452
c_chr_uni 6619041
c_chr_multi 2779733
c_chr_sum 9398774
c_chr_sum_check 18797548
Writing to dataframe...
c_name WT_G1_day1_ovn_SS_aux-F_tc-F_rep2_tech1
c_all 10009120
c_MK2_uni 1042420
c_MK2_multi 307317
c_MK2_sum 1349737
c_MK2_sum_check 2699474
c_chr_uni 6866366
c_chr_multi 1793017
c_chr_sum 8659383
c_chr_sum_check 17318766
Writing to dataframe...
c_name WT_G1_day1_tcn_SS_aux-F_tc-F_rep1_tech1
c_all 25720373
c_MK2_uni 1349853
c_MK2_multi 4608823
c_MK2_sum 5958676
c_MK2_sum_check 11917352
c_chr_uni 8283008
c_chr_multi 11478689
c_chr_sum 19761697
c_chr_sum_check 39523394
Writing to dataframe...
c_name WT_G1_day1_tcn_SS_aux-F_tc-F_rep2_tech1
c_all 24063950
c_MK2_uni 1304628
c_MK2_multi 4304410
c_MK2_sum 5609038
c_MK2_sum_check 11218076
c_chr_uni 7746887
c_chr_multi 10708025
c_chr_sum 18454912
c_chr_sum_check 36909824
Writing to dataframe...
c_name WT_Q_day7_ovn_N_aux-F_tc-F_rep1_tech1
c_all 18858614
c_MK2_uni 8740540
c_MK2_multi 585307
c_MK2_sum 9325847
c_MK2_sum_check 18651694
c_chr_uni 8502909
c_chr_multi 1029858
c_chr_sum 9532767
c_chr_sum_check 19065534
Writing to dataframe...
c_name WT_Q_day7_ovn_N_aux-F_tc-F_rep2_tech1
c_all 17445726
c_MK2_uni 6353848
c_MK2_multi 448111
c_MK2_sum 6801959
c_MK2_sum_check 13603918
c_chr_uni 9697530
c_chr_multi 946237
c_chr_sum 10643767
c_chr_sum_check 21287534
Writing to dataframe...
c_name WT_Q_day7_ovn_SS_aux-F_tc-F_rep1_tech1
c_all 9515191
c_MK2_uni 2553353
c_MK2_multi 611511
c_MK2_sum 3164864
c_MK2_sum_check 6329728
c_chr_uni 4374618
c_chr_multi 1975709
c_chr_sum 6350327
c_chr_sum_check 12700654
Writing to dataframe...
c_name WT_Q_day7_ovn_SS_aux-F_tc-F_rep2_tech1
c_all 8394823
c_MK2_uni 2519133
c_MK2_multi 611776
c_MK2_sum 3130909
c_MK2_sum_check 6261818
c_chr_uni 3403427
c_chr_multi 1860487
c_chr_sum 5263914
c_chr_sum_check 10527828
Writing to dataframe...
c_name WT_Q_day7_tcn_N_aux-F_tc-F_rep2_tech1
c_all 29909019
c_MK2_uni 14119767
c_MK2_multi 2239800
c_MK2_sum 16359567
c_MK2_sum_check 32719134
c_chr_uni 10065665
c_chr_multi 3483787
c_chr_sum 13549452
c_chr_sum_check 27098904
Writing to dataframe...
c_name WT_Q_day7_tcn_SS_aux-F_tc-F_rep2_tech1
c_all 27062659
c_MK2_uni 15976322
c_MK2_multi 1965855
c_MK2_sum 17942177
c_MK2_sum_check 35884354
c_chr_uni 3997078
c_chr_multi 5123404
c_chr_sum 9120482
c_chr_sum_check 18240964
Writing to dataframe...
c_name WT_Q_day8_tcn_N_aux-F_tc-F_rep1_tech1
c_all 27401884
c_MK2_uni 9789534
c_MK2_multi 2039370
c_MK2_sum 11828904
c_MK2_sum_check 23657808
c_chr_uni 11645493
c_chr_multi 3927487
c_chr_sum 15572980
c_chr_sum_check 31145960
Writing to dataframe...
c_name WT_Q_day8_tcn_N_aux-F_tc-F_rep2_tech1
c_all 27455219
c_MK2_uni 9649998
c_MK2_multi 2213197
c_MK2_sum 11863195
c_MK2_sum_check 23726390
c_chr_uni 11457622
c_chr_multi 4134402
c_chr_sum 15592024
c_chr_sum_check 31184048
Writing to dataframe...
c_name WT_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1
c_all 26476817
c_MK2_uni 15271102
c_MK2_multi 2391643
c_MK2_sum 17662745
c_MK2_sum_check 35325490
c_chr_uni 2941561
c_chr_multi 5872511
c_chr_sum 8814072
c_chr_sum_check 17628144
Writing to dataframe...
c_name WT_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1
c_all 27471330
c_MK2_uni 16159674
c_MK2_multi 2304666
c_MK2_sum 18464340
c_MK2_sum_check 36928680
c_chr_uni 3128807
c_chr_multi 5878183
c_chr_sum 9006990
c_chr_sum_check 18013980
❯ cat outfiles_htseq-count/calculate_uni-multimappers-etc.UT_prim_UMI.txt
sample sample_total Mito-KL-20S_all Mito-KL-20S_uni Mito-KL-20S_multi SC-I-XVI_all SC-I-XVI_uni SC-I-XVI_multi
n3-d_Q_day7_tcn_N_aux-T_tc-F_rep1_tech1 28593750 15840366 13723802 2116564 12753384 9618005 3135379
n3-d_Q_day7_tcn_N_aux-T_tc-F_rep2_tech1 29274110 18124271 15496048 2628223 11149839 7740567 3409272
n3-d_Q_day7_tcn_N_aux-T_tc-F_rep3_tech1 32294104 17369871 14561827 2808044 14924233 10839993 4084240
n3-d_Q_day7_tcn_SS_aux-T_tc-F_rep1_tech1 29462906 18898366 17008920 1889446 10564540 5254921 5309619
n3-d_Q_day7_tcn_SS_aux-T_tc-F_rep2_tech1 30485089 20964496 18942478 2022018 9520593 4284572 5236021
n3-d_Q_day7_tcn_SS_aux-T_tc-F_rep3_tech1 24769078 15988150 14275293 1712857 8780928 4164893 4616035
o-d_Q_day7_tcn_N_aux-T_tc-F_rep1_tech1 26199413 17062082 14487580 2574502 9137331 5897639 3239692
o-d_Q_day7_tcn_N_aux-T_tc-F_rep2_tech1 25614430 17857348 15243591 2613757 7757082 4329477 3427605
o-d_Q_day7_tcn_SS_aux-T_tc-F_rep1_tech1 27546890 15329279 11997347 3331932 12217611 3428982 8788629
o-d_Q_day7_tcn_SS_aux-T_tc-F_rep2_tech1 27650067 16428956 13663469 2765487 11221111 3564552 7656559
r1-n_Q_day8_tcn_N_aux-F_tc-F_rep1_tech1 26074381 12042994 10085027 1957967 14031387 10241422 3789965
r1-n_Q_day8_tcn_N_aux-F_tc-F_rep2_tech1 27859800 13035770 10797819 2237951 14824030 10653110 4170920
r1-n_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1 28872243 19144655 16807216 2337439 9727588 3483824 6243764
r1-n_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1 26452129 18418579 16482900 1935679 8033550 2959398 5074152
r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1 14862518 3782897 1751924 2030973 11079621 7189320 3890301
r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1 18842139 4511200 2040193 2471007 14330939 9406289 4924650
r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1 14693909 6382649 3677835 2704814 8311260 4644448 3666812
r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1 17701239 7547037 4535393 3011644 10154202 6119775 4034427
r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1 17676487 5558816 2748189 2810627 12117671 7713092 4404579
r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1 18673410 5725360 2774145 2951215 12948050 8210263 4737787
r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1 20109413 11975782 8170752 3805030 8133631 3853707 4279924
r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1 27172906 14755847 7306541 7449306 12417059 3856299 8560760
r6-n_G1_day1_tcn_SS_aux-F_tc-F_rep1_tech1 26649217 6725997 2288830 4437167 19923220 10633162 9290058
r6-n_G1_day1_tcn_SS_aux-F_tc-F_rep2_tech1 26995608 6311404 2223334 4088070 20684204 11425076 9259128
r6-n_Q_day8_tcn_N_aux-F_tc-F_rep1_tech1 28279689 11109577 9184377 1925200 17170112 13364739 3805373
r6-n_Q_day8_tcn_N_aux-F_tc-F_rep2_tech1 27494489 12881785 10814101 2067684 14612704 10933792 3678912
r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1 37273438 19632166 14994726 4637440 17641272 3932961 13708311
r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech2 31127425 16368756 12492174 3876582 14758669 3226890 11531779
r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1 29051610 18592993 16215412 2377581 10458617 4427289 6031328
t4-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1 18639826 4153045 1538212 2614833 14486781 8938957 5547824
t4-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1 17426630 3711589 1326048 2385541 13715041 8391340 5323701
t4-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1 19276505 8655598 5191638 3463960 10620907 6151066 4469841
t4-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1 19092950 8748526 5445342 3303184 10344424 6102549 4241875
t4-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1 20391336 5527031 2240497 3286534 14864305 8515633 6348672
t4-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1 20894588 5893086 2541675 3351411 15001502 9126826 5874676
t4-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1 17788422 10597928 7287411 3310517 7190494 3628475 3562019
t4-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1 19014451 11736913 8176542 3560371 7277538 3533077 3744461
WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1 17528651 3316447 1291305 2025142 14212204 9170938 5041266
WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1 14354209 2854219 1025775 1828444 11499990 6997554 4502436
WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1 17870971 8569374 4821046 3748328 9301597 4704206 4597391
WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1 18187692 8468466 4874871 3593595 9719226 5105886 4613340
WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1 16268286 4664659 2069852 2594807 11603627 6924408 4679219
WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1 18162697 5201273 2144943 3056330 12961424 7185078 5776346
WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1 18353221 11322507 7388417 3934090 7030714 2984238 4046476
WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech2 29105695 16516973 8020750 8496223 12588722 3374316 9214406
WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1 16959938 10387936 7036884 3351052 6572002 2789045 3782957
WT_G1_day1_ovn_N_aux-F_tc-F_rep1_tech1 15634566 415391 353542 61849 15219175 13188385 2030790
WT_G1_day1_ovn_N_aux-F_tc-F_rep2_tech1 15755143 701134 625995 75139 15054009 12953728 2100281
WT_G1_day1_ovn_SS_aux-F_tc-F_rep1_tech1 10723500 1324726 753929 570797 9398774 6619041 2779733
WT_G1_day1_ovn_SS_aux-F_tc-F_rep2_tech1 10009120 1349737 1042420 307317 8659383 6866366 1793017
WT_G1_day1_tcn_SS_aux-F_tc-F_rep1_tech1 25720373 5958676 1349853 4608823 19761697 8283008 11478689
WT_G1_day1_tcn_SS_aux-F_tc-F_rep2_tech1 24063950 5609038 1304628 4304410 18454912 7746887 10708025
WT_Q_day7_ovn_N_aux-F_tc-F_rep1_tech1 18858614 9325847 8740540 585307 9532767 8502909 1029858
WT_Q_day7_ovn_N_aux-F_tc-F_rep2_tech1 17445726 6801959 6353848 448111 10643767 9697530 946237
WT_Q_day7_ovn_SS_aux-F_tc-F_rep1_tech1 9515191 3164864 2553353 611511 6350327 4374618 1975709
WT_Q_day7_ovn_SS_aux-F_tc-F_rep2_tech1 8394823 3130909 2519133 611776 5263914 3403427 1860487
WT_Q_day7_tcn_N_aux-F_tc-F_rep2_tech1 29909019 16359567 14119767 2239800 13549452 10065665 3483787
WT_Q_day7_tcn_SS_aux-F_tc-F_rep2_tech1 27062659 17942177 15976322 1965855 9120482 3997078 5123404
WT_Q_day8_tcn_N_aux-F_tc-F_rep1_tech1 27401884 11828904 9789534 2039370 15572980 11645493 3927487
WT_Q_day8_tcn_N_aux-F_tc-F_rep2_tech1 27455219 11863195 9649998 2213197 15592024 11457622 4134402
WT_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1 26476817 17662745 15271102 2391643 8814072 2941561 5872511
WT_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1 27471330 18464340 16159674 2304666 9006990 3128807 5878183