[Bioc-sig-seq] readAligned and SAM format

[Martin Morgan]

"Hattem, Gaye" <GLH at stowers.org> writes:

> Does the readAligned function in ShortRead currently support the SAM
> format? The vignette mentions that Short Read has been extended to
> include several formats and lists the SAM format but I don't see
> this option documented anywhere.

Hi Gaye -- 

SAM is not yet supported, but will be in the next release (my
preference is for the binary variant, BAM). MAQ and Bowtie-style input
is available.

Martin


> Gaye Hattem
> Stowers Institute for Medical Research
> glh at stowers dot org
>
>
>
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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