This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Aligning multiple Fastq files using Bowtie2

I want to align multiple paired end Fastq files belonging to different samples (RNA-seq reads) using Bowtie2. Bowtie allows alignment for multiple Fastq files at once but produces only one output SAM file specified by -S flag. I wanted to know whether this output file would be useful for downstream applications. Thanks.

rna-seq bowtie2 alignment fastq
• 2,826 views • link
updated by WouterDeCoster WouterDeCoster • written by deepak18 • deepak18

Also if it is possible then how can I get multiple SAM output files each corresponding to one sample.

• 0 views • link
written by deepak18 • deepak18

1 answer

As far as I know, no, it's not possible to have multiple samples/fastq files result in multiple sam/bam files (or add different read groups). Why would you want to do this?

Just run bowtie separately for each sample. Don't make this more complicated than necessary.

• 0 views • link
written by WouterDeCoster WouterDeCoster

Thank you for your valuable reply.

• 0 views • link
written by deepak18 • deepak18

Log in to answer this question.

More posts like this