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chr.sub #4

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walaj opened this issue Mar 20, 2016 · 5 comments
Open

chr.sub #4

walaj opened this issue Mar 20, 2016 · 5 comments

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@walaj
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walaj commented Mar 20, 2016

Propose removing this. Not sure what the issue is with having "chr" in the seqinfo, and it seems like if there is a problem, a more general solution should be used (e.g. manipulate seqinfo however you like on your own, and then set with seqinfo<- )

@mskilab
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mskilab commented Mar 20, 2016

sure agree in principle

this basically applies to gTrack that we build off external files - e.g. .bam, .wig., .bw etc where you can't manipulate the seqinfo in that manner

in practice "chr" are a <> since a lot of UCSC tracks will be stored as .bw with chr prefixes and then you're trying to plot them against your broad .bam which has no "chr" ...

open to other fixes .. but we should have a solution for this

@KhagayN
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KhagayN commented Dec 5, 2016

if chr.sub is removed, how would we remove the "chr" prefixes from external files such as .bam, .wig, .bw where they can't be manipulated by using the seqinfo function?

@mskilab
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mskilab commented Dec 6, 2016 via email

@mskilab
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mskilab commented Dec 6, 2016 via email

@KhagayN
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KhagayN commented Dec 6, 2016

ahh, especially as you mentioned on Mar 20, when plotting these tracks against broad .bam that has no "chr". Sounds like keeping chr.sub is a good idea but, include tests that chr.sub works for the external files that can be inputted.

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