"Hattem, Gaye" <[email protected]> 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 > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Martin Morgan 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
