Hi Yan, Yes, "Slice BAM" is like a filter, so the output should be smaller if some of the data mapped to regions outside of the intervals (entirely - no overlap). You can run flagstat on both files and compare the two numbers to see the difference/what was filtered. For QC-passed/failed - this is a great question without a simple answer (as it has some history). Or so I thought. Then, I found a very simple post by Prof Albert on Biostar addressing the same question, that I think is about as good as it can get! (Main point = can safely ignore) http://www.biostars.org/p/16100/ Hope this helps! Jen Galaxy team On 9/12/13 10:11 PM, Yan He wrote:

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

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