[Bioc-devel] readGAlignmentsList and read groups

Valerie Obenchain vobencha at fhcrc.org
Thu Dec 5 21:56:51 CET 2013


You're right, currently the only 'automatic' grouping is by pairs.

For single-end, grouping by tag would straightforward (assuming this is 
a "match on value" not a procedure of checking bit flags etc.).

For paired-end I'm assuming you want the records first grouped by pairs 
then grouped by tag? Maybe it's worth thinking about putting tags common 
to pairs on the outer list elements vs inner. For data are that aren't 
'too large' this would allow easier sorting/splitting.


On 12/05/2013 11:19 AM, Michael Lawrence wrote:
> The function readGAlignmentsList[FromBam] sounds general, but it's purpose
> currently seems specific to grouping by read pair. What about other types
> of grouping, in particular the RG tag? This would be helpful when dealing
> with sequencing data for many amplicons.
> Just an idea.
> Michael
> 	[[alternative HTML version deleted]]
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Valerie Obenchain

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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E-mail: vobencha at fhcrc.org
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