On Tue, Apr 5, 2011 at 2:01 PM, Slim Sassi 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" 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
>> > 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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>
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