On Tue, Apr 5, 2011 at 2:01 PM, Slim Sassi ssassi@ccib.mgh.harvard.edu wrote:
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
That information is not in the FASTQ files, so it will not be in the BAM files, generally.
% mapped
That information assumes that the aligner writes the the unaligned reads to the BAM file. Tophat does not do that.
% reads in exons/introns/intergenic regions
That is not something that flatstats provides. However, there are a number of other tools that could be coerced to give you this type of information (including Galaxy, probably).
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.
For this task, you may have to write some code unless someone else on the list is aware of a package that does this for RNA-seq data.
Thanks Slim
On Apr 5, 2011, at 1:50 PM, Sean Davis wrote:
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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