view Bowtie2 alignment results

Question

[lkianmehr]

Does anybody know that how do I to get the results of Bowtie2 after alignment? is it possible?

[Benn]

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.

[lkianmehr]

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

[h.mon]

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.

Answer 1

[GenoMax]

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.

[lkianmehr]

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