Stat summary on reads alignment after bowtie2

[lgiloteaux]

Hi,

I ran bowtie2 on a sample, after running I got this info on the terminal:

194885413 reads; of these:
194885413 (100.00%) were unpaired; of these:
39117955 (20.07%) aligned 0 times
103311806 (53.01%) aligned exactly 1 time
52455652 (26.92%) aligned >1 times
79.93% overall alignment rate
[samopen] SAM header is present: 25 sequences.

I did it on another sample but didn't get a chance to see these stats
I ran a bamtools stats and samtools flagstat on the alignment.bam file but this is not giving me the number of reads "aligned exactly 1 time" or "aligned >1 times"

How can I retrieve this info after bowtie ends

Thanks,

Ludovic

[dpryan]

I've seen people ask this often enough that I just wrote a python script using pysam to do it. It currently only handles single-end reads, but I can change that quite simply.

[lgiloteaux]

Thanks a lot !