Feature idea/request: strand aware igvtools

[Steve Lianoglou]

Hi,

Somehow related to issue #14[1] (but not entirely), I was just
thinking it would be handy if `igvtools count BAM` could take a
`strand` option so it only produces a TDF for coverage on forward (or
reverse) strand.

Thanks,
-steve

[1] Issue #14: http://code.google.com/p/igv/issues/detail?id=14

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Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

[Jim Robinson]

Steve, we're working on this now, but with a strand option that computes coverage for both strands  (not one or the other).   Do you really have a case where you want one, and only one, strand?

Jim

[Steve Lianoglou]

Hi Jim,

The use case I have is to be able to see a coverage-like track but to
know which strand the coverage is coming from and the only way I
thought I could do that and display it in IGV is to make a tdf for the
positive and negative strands separately.

From what you describe, I don't understand how the feature you are
working on now differs from the normal `count`-ing?

Are you making a new type of *.tdf (say) that displays coverage on the
positive strand above the y axis, and the coverage from the negative
strand below the axis (ie. as negative values), or something? That'd
be cool :-)

-steve

[Jim Robinson]

Steve, yes, that is exactly it. It will be a 2-value TDF. TDF
format already supports multiple values for a location. We'll also
give the option of computing this by read strand, or by the
"first-of-pair" strand. The latter is important for many paired-end
libraries.

Jim

> ....

[Steve Lianoglou]

That's awesome.

Looking forward to that feature!

-steve

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