samstat output is different than bowtie2 stats
Closed this issue · 2 comments
bounlu commented
The output stats from bowtie2 and samstat on the same bam file are different:
bowtie2:
18657869 reads; of these:
18657869 (100.00%) were unpaired; of these:
1995321 (10.69%) aligned 0 times
12773937 (68.46%) aligned exactly 1 time
3888611 (20.84%) aligned >1 times
89.31% overall alignment rate
samstat:
any explanation?
TimoLassmann commented
Samstat works only on SAM/BAM lines that represent primary alignments and excludes all reads that fail platform/vendor quality checks. I suspect that this is where the discrepancies come from.
bounlu commented
I see, you are using the flag -F 768. Thanks for the info.