[Bioc-devel] Rsamtools BAM > SAM?

Martin Morgan mtmorgan at fhcrc.org
Thu Dec 5 09:30:50 CET 2013

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.


> Regards,
> _Taku
> Taku Tokuyasu
> Computational Biology Core
> UCSF Helen Diller Family Comprehensive Cancer Center

Computational Biology / Fred Hutchinson Cancer Research Center
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