Hi Jen and other galaxy-users,

I was using “Slice BAM” tool on Galaxy to get the alignment overlap with the targeted intervals. After I got the output BAM file, I used “flagstat” to get the detailed information of the output BAM file. What I got from “flagstat” is as following.

“13704486 + 0 in total (QC-passed reads + QC-failed reads)

0 + 0 duplicates

2989995 + 0 mapped (21.82%:-nan%)

13704486 + 0 paired in sequencing”

What’s the QC-passed reads? What’s the mapped reads? Should I only get the mapped reads to the targeted intervals? I am very confused. Any help is highly appreciated! Thanks a lot!

Best wishes,

Yan