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  • Gonzalo S Nido
  • wgbs-pipelinewgbs-pipeline
  • Issues
  • #3
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Issue created Sep 04, 2020 by Gonzalo S Nido@gni042Owner

Fix extract methylation MT/LAMBDA script

As per now, it is executed twice, once for the MT chr and once for the LAMBDA. The script apps/ext_chr_srt.py should accept multiple command line arguments, each being a chromosome.

IDEAS

  • Remove the test for "Bismark" start of line on each iteration, leave it just for the first line
  • Open one file handle for each input chromosome and output reads there

This script is executed in the main pipeline (wgbs-pipeline.sh) and that call will need to be updated consequentially.

Edited Sep 04, 2020 by Gonzalo S Nido
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