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<code>--sam-RG</code> flag adds <code>RG</code> line to header, but does not set <code>RG</code> tag on alignments

Status: Open.

#143 In BenLangmead/bowtie;

· joshuagryphon opened on Jan 24, 2025

Bowtie runs successfully without the --best option but fails when the --best option is included

Status: Open.

#142 In BenLangmead/bowtie;

· santataRU opened on Nov 27, 2024

bowtie for short reads

Status: Open.

#141 In BenLangmead/bowtie;

· alessandromacc opened on Jul 12, 2024

bowtie alignmnet produces sam bam files sizes for different fastq files

Status: Open.

#140 In BenLangmead/bowtie;

· deepthi-omics opened on May 24, 2024

secondary alignment flag

Status: Open.

#139 In BenLangmead/bowtie;

· adthrasher opened on Oct 30, 2023

Compatibility of Bowtie1 (v1.2.0 or later) with Tophat2

Status: Open.

#138 In BenLangmead/bowtie;

· rason81 opened on Sep 4, 2023

Is there an equivalent of "Bowtie2 --very-sensitive" for Bowtie1 [suggested label = Question]

Status: Open.

#137 In BenLangmead/bowtie;

· AndreaMariani-AM opened on Mar 7, 2023

Cline paired 2 (fw:1, sam:1) test aborted with -Wp,-D_GLIBCXX_ASSERTIONS

Status: Open.

#136 In BenLangmead/bowtie;

· junaruga opened on Feb 17, 2023

Some reference entries show up as duplicates

Status: Open.

#135 In BenLangmead/bowtie;

· DeadlineWasYesterday opened on Jul 13, 2022

Questions about tracking the history of building index

Status: Open.

#134 In BenLangmead/bowtie;

· Youpu-Chen opened on Jun 29, 2022

-m setting not outputting a sam file with an -NH tag

Status: Open.

#133 In BenLangmead/bowtie;

· elayton13 opened on May 20, 2022

Error: reads file does not look like a FASTQ file

Status: Open.

#129 In BenLangmead/bowtie;

· amitjavilaventura opened on Feb 7, 2022