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YeoLab / gscripts

General Use Scripts and Helper functions
MIT License
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remove reptitive regions on paired-end #58

Closed olgabot closed 9 years ago

olgabot commented 9 years ago

to fix this: https://github.com/YeoLab/gscripts/issues/57

should remove repetitive regions on paired-end too, so that the paired end and single end are comparable

olgabot commented 9 years ago

ready to merge

olgabot commented 9 years ago

doesn't work on single-end reads.... I'm an idiot and in my testing copied my PE manifest file to the SE name. stay tuned.

gpratt commented 9 years ago

Try to do a rebase / pull I updated repetitive elements removal to use star, might make your job a bit easier/ it will need to be integrated anyway. On Feb 21, 2015 11:17 AM, "Olga Botvinnik" notifications@github.com wrote:

doesn't work on single-end reads.... I'm an idiot and in my testing copied my PE manifest file to the SE name. stay tuned.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/pull/58#issuecomment-75387567.

olgabot commented 9 years ago

just rebased

olgabot commented 9 years ago

I'll try doing a merge ...

olgabot commented 9 years ago

caveat: the paired end stringent jobs using trimgalore doesn't map with STAR as the single end no trimgalore one does