Manuscript and Data

This repository contains source code developed for this manuscript:

Selfish mutations dysregulating RAS-MAPK signaling are pervasive in aged human testes

Geoffrey J. Maher, Hannah K. Ralph, Zhihao Ding, Nils Koelling, Hana Mlcochova, Eleni Giannoulatou, Pawan Dhami, Dirk S. Paul, Stefan H. Stricker, Stephan Beck, Gilean McVean, Andrew OM Wilkie, Anne Goriely

The raw FASTQ files can be downloaded from here. The VCF with pileup counts per sample per site can be downloaded here.

User guide

• Scan reads in FASTQ for sample. Assign amplicon ID to each read using a kmer search algorithm.

  python parse_primer.py --fastq --sample sampleName
      

• Alignment for each sample.

  bwa mem -R "@RG\tID:$ID\tSM:$SM\tLB:$LB" $ref $read1 $read2 > $sam
      

• Pileup for all sites for each sample.

  python parse_primer.py --pileup --sample sampleName
      

• Combine pileups of all samples and write out result datasets.

  python parse_primer.py --sum
      

• Generating files/plots for each amplicon to assist QC on input signals.

  python parse_primer.py --agg --amp ampliconName
      

• Call elevated alleles for amplicon.

  python parse_primer.py --call --amp ampliconName
      

Meta Data

File Name	Description
meta/samplelist	A list of IDs of all samples
meta/fastq.index	A list input fastq files
meta/amplicons.csv	Meta information for the amplicons
meta/sample_seq.csv	Meta information for sequencing libraries