[Bioc-devel] Rsamtools BAM > SAM?
mtmorgan at fhcrc.org
Thu Dec 5 09:30:50 CET 2013
On 12/04/2013 11:17 PM, Taku Tokuyasu wrote:
> 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
> 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.
> Taku Tokuyasu
> Computational Biology Core
> UCSF Helen Diller Family Comprehensive Cancer Center
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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