Sean, I only wanted to start collecting stats with flagstats but knew that I needed something else to get everthing needed. I would like to know: % that didn't pass QC % mapped % reads in exons/introns/intergenic regions
and then, knowing that this is more complicated, I wanted to measure bias within transcripts (for example 3' versus 5'). Of course I am assuming that there is a consistent bias. Thanks Slim On Apr 5, 2011, at 1:50 PM, Sean Davis wrote: > > On Apr 5, 2011 1:05 PM, "Slim Sassi" <[email protected]> wrote: > > > > Sean, > > You are correct, I did use tophat. Can you or anyone suggest a program for > > BAM/SAM stats where the alignment was done with tophat > > > > Slim, > > What stats do you want to capture? The output you gave for flagstats is > correct for single-end tophat alignments. All reads are aligned, none are > paired, none are marked as duplicates. > > Sean > > > Thanks > > Slim > > On Apr 5, 2011, at 12:51 PM, Sean Davis wrote: > > > > > 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. > >
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