Question: Bowtie2 output alignments and non-alignments in same file
0
gravatar for zhangzhenyusz
19 months ago by
zhangzhenyusz20 wrote:

Hi everybody,

I'm using Bowtie2 and I'm trying to output the alignments to a SAM file and unmapped to fastq file. I know --no-unal option make sam file only contain the mapped reads; however, my fastq files will have zero content because all unmapped reads are omitted. Does anyone know any option(s) to fulfil both goals.

Thank you!

rna-seq bowtie2 • 610 views
ADD COMMENTlink modified 19 months ago by Brian Bushnell16k • written 19 months ago by zhangzhenyusz20
0
gravatar for Brian Bushnell
19 months ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

I've revised your post to a question, as it is not a tool post. Also, Bowtie2 is not a good tool for RNA-seq since it is not splice-aware.

You can filter out unmapped reads from the sam file after the fact, and convert the filtered reads to fastq, with BBMap's reformat.sh:

reformat.sh in=reads.sam out=mapped.sam mappedonly
reformat.sh in=reads.sam out=unmapped.fq unmappedonly

Or use BBMap in the first place (which is splice aware) like this:

bbmap.sh in=reads.fq outm=mapped.sam outu=unmapped.fq ref=ref.fa maxindel=200k
ADD COMMENTlink written 19 months ago by Brian Bushnell16k

Oh I'm actually on bacteria. Thank you for the BBMap one.

ADD REPLYlink written 19 months ago by zhangzhenyusz20

My mistake; for bacteria Bowtie2 is fine.

ADD REPLYlink written 19 months ago by Brian Bushnell16k
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