It would be appreciated to know where the current counting methods fall
short; i.e., why htseq-count is necessary.

Thanks,
Michael


On Thu, Dec 5, 2013 at 12:30 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 12/04/2013 11:17 PM, Taku Tokuyasu wrote:
>
>> Hello,
>>
>> We are trying to support NGS pipelines with SAM input to htseq-count, w/o
>> requiring a samtools install.  Has Rsamtools implemented / planned any
>> support
>> for BAM to SAM conversion?  I notice this has been requested before (e.g.
>> May
>> 2012,
>> http://comments.gmane.org/gmane.science.biology.
>> informatics.conductor/41344), so
>> I was wondering if there were any updates on this.
>>
>
> I added this to Rsamtools 1.15.14; this requires other package
> dependencies to be current. I had delayed adding this because it seems a
> step backward, to a relatively inefficient representation.
>
> Other counting alternatives not requiring coercion to SAM files are
> GenomicAlignments::summarizeOverlaps (acting on BamFile / BamViews /
> GAlignments / GAlignmentPairs, counting bins as GRanges / GRanges list from
> TxDb or standard GTF etc files via rtracklayer::import) and
> Rsubread::featureCount (SAM or BAM files, built-in or GTF or SAF annotation
> files).
>
> Please let me know if there are issues with the implementation.
>
> Martin
>
>
>> Regards,
>>
>> _Taku
>>
>> Taku Tokuyasu
>> Computational Biology Core
>> UCSF Helen Diller Family Comprehensive Cancer Center
>>
>>
>>
>
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