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Question: view Bowtie2 alignment results
2
gravatar for lkianmehr
2.5 years ago by
lkianmehr • 50
France
lkianmehr • 50 wrote:

Does anybody know that how do I to get the results of Bowtie2 after alignment? is it possible?
bowtie alignment results • 2.0k views
ADD COMMENT • link •
modified 2.5 years ago by h.mon ♦ 32k • written 2.5 years ago by lkianmehr • 50
1

I am not sure what you're asking here. Please explain in more detail what you did and what you are trying to achieve. Which code you use, etc. Results of alignments are usually put in a BAM file, but your question is too vague to really know what you are asking. A BAM file can be viewed in IGV.

ADD REPLY • link modified 2.5 years ago • written 2.5 years ago by Benn ♦ 8.1k

I did the alignment of reads parallel on the server but I don't have their results summary, so I need to see it, what should I do

ADD REPLY • link written 2.5 years ago by lkianmehr • 50

If by results you mean the alignment in SAM format, you have either to redirect bowtie2 command to a file (bowtie2 ... > output.sam), or use bowtie2 ... -S output.sam. By default, bowtie2 outputs to stdout.

ADD REPLY • link written 2.5 years ago by h.mon ♦ 32k
2
gravatar for GenoMax
2.5 years ago by
GenoMax ♦ 95k
United States
GenoMax ♦ 95k wrote:

Do you have a file with the alignments? You can use Qualimap or samtools stats (to get just a text summary) of the alignment stats.
ADD COMMENT • link modified 2.5 years ago • written 2.5 years ago by GenoMax ♦ 95k

I have a sam file, I did samtools stats but it didn't work for all sam files, is it needed to do anything before that? for example convert to bam, sort, index and then run samtools stats or not?

thanks in advance

ADD REPLY • link written 2.5 years ago by lkianmehr • 50
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