Question: Aligning multiple Fastq files using Bowtie2
0
gravatar for deepak18
11 months ago by
deepak1810
deepak1810 wrote:

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 alignment fastq bowtie2 • 444 views
ADD COMMENTlink modified 11 months ago by WouterDeCoster44k • written 11 months ago by deepak1810

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

ADD REPLYlink written 11 months ago by deepak1810
0
gravatar for WouterDeCoster
11 months ago by
Belgium
WouterDeCoster44k wrote:

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.

ADD COMMENTlink written 11 months ago by WouterDeCoster44k

Thank you for your valuable reply.

ADD REPLYlink written 11 months ago by deepak1810
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