Bowtie Output Information

[lwhitmore]

Default bowtie

Hi I am just wondering if you run bowtie with -v 0 (meaning no mismatches are allowed in the alignment) and -a (meaning mulitple alignments are allowed) is the last column the number of times the read maps to the genome? 0 indicating that the alignment is unique?

[swbarnes2]

I'm pretty sure that bowtie's default alignment will output one line for each aligned read, and no lines for each unaligned read, so you could do a wc -l on the file, and just count how many lines there are, and that's how many reads aligned.

[psurana]

Hi psurana,

This does not answer your question directly but may help you out: Bowtie can output alignment in the sam format. So if you can not find a solution to your problem, you may redo the alignment with option -S (or --sam)

Douglas
www.contigexpress.com

Thanks, I might try that.

[DZhang]

Hi psurana,

This does not answer your question directly but may help you out: Bowtie can output alignment in the sam format. So if you can not find a solution to your problem, you may redo the alignment with option -S (or --sam)

Douglas

https://www.contigexpress.com

[psurana]

samtools flagstat a.bam

I have the bowtie output in the default format not the sam format. Is there a way to convert the already existing bowtie default output to sam format which I could then convert to bam of course.

Thanks

[fabrice]

samtools flagstat a.bam

[psurana]

Does anyone know how to find out % aligned reads from a bowtie output file? Is there a command to do it? Is it there somewhere in the file? I did not save this information for my output files and would like to get it now.

Thanks,
Priyanka Surana