Hi, Slim. My guess is that you used an aligner that outputs only aligned reads (tophat, for example) and that the input was single-ended. If that is the case, then what you see below is exactly as expected. If not, then you might need to be more specific about how you generated the BAM file.
Sean On Tue, Apr 5, 2011 at 12:31 PM, Slim Sassi <[email protected]> wrote: > Hello, > I tried to use NGS: SAM Tools ->flagstat on a BAM files for basic stats, but > I got results like you see below. It doesn't seem to be working. Any > suggestions? > 26584869 in total > > 0 QC failure > 0 duplicates > 26584869 mapped (100.00%) > 0 paired in sequencing > 0 read1 > 0 read2 > 0 properly paired (-nan%) > 0 with itself and mate mapped > 0 singletons (-nan%) > 0 with mate mapped to a different chr > 0 with mate mapped to a different chr (mapQ>=5) > > Thanks > Slim > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
