On 04/12/2010 09:35 AM, burak kutlu wrote: > Hi Is there a way to create a SAM file from the output of scanBam > from Rsamtools? The reason we would like to do is use IGV to > visualize a subset of regions in a large Bam file using load2newIGV > function from SRAdb. For this, we will need to put the list structure > back to SAM format. Please let me know if this is enough to give you
no not at the moment; this is on the to do list. There is filterBam which does a round-trip (no R interaction) though here it might make as much sense to use samtools from the command line. Martin > an idea what we are trying to achieve. Thanks in advance -burak > > _______________________________________________ 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
