bedtools needs genome - Githubissues

biocore-ntnu / epic

(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER

http://bioepic.readthedocs.io

MIT License

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bedtools needs genome #6

Closed daler closed 8 years ago

daler commented 8 years ago

bedtools bamtobed needs a genome file on recent (within the last few years?) versions of bedtools. Using BAM files as input is not possible with the bedtools versions available in bioconda due to this call to bedtools.

endrebak commented 8 years ago

Nice catch, now next on my todo. Thanks to your last PR, this will be super easy to solve with the genome size files from pkg_utils.

endrebak commented 8 years ago

The bug was actually that I used bedToBam not bamToBed. This was fixed a while ago, but I must have gotten confused by git. (Wonder what other regressions I introduced?) Thanks again.

c-guzman commented 8 years ago

This is still a problem using epic version 0.0.6 which is the latest version available on anaconda. Epic still uses bedtobam.