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!
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