On Apr 5, 2011 1:05 PM, "Slim Sassi" ssassi@ccib.mgh.harvard.edu 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 ssassi@ccib.mgh.harvard.edu
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
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