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BIMSBbioinfo / pigx_rnaseq

Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline
GNU General Public License v3.0
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replace export.bw with a better candidate #91

Closed frenkiboy closed 3 years ago

frenkiboy commented 3 years ago

Candidates:

  1. bam2bw https://github.com/cancerit/cgpBigWig

  2. wiggleTools - samtools view test/bam.bam | wiggletools sam - https://github.com/Ensembl/WiggleTools don't know the exact command for conversion, but should be possible

  3. megadepth - I would use this one because of the name This one has both memory and time, and it beats rtracklayer by a lot https://github.com/LieberInstitute/megadepth

  4. deeptools is an option http://deeptools.readthedocs.io/en/latest/content/tools/bamCoverage.html

I don't know how these tools scale with data (memory and cpu)

borauyar commented 3 years ago

https://github.com/BIMSBbioinfo/pigx_rnaseq/issues/69#issue-548917030

borauyar commented 3 years ago

Replaced export.bw with deeptools-bamCoverage in version 0.0.15 see: https://github.com/BIMSBbioinfo/pigx_rnaseq/commit/f9660de48b3eb6ca48990717db9224c72b9c20ba