Skip to content

Handle polyA processing in input preparation script

BIOPZ-Katsantoni Maria requested to merge input_features into master
  • fixes some functions in labkey_to_snakemake.py
  • add optional argument for trimming polyA tails; they are trimmed as follows:
    • if mate is sense, oligo-A is added to sample table for cutadapt rule to trim
    • if mate is antisense, oligo-T is added to sample table for cutadapt rule to trim
    • if option is set to --trim_polya, oligo-X stretch is added to sample table and cutadapt will not trim

Closes #37 (closed)

Edited by Alex Kanitz

Merge request reports