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  • BIOPZ-Katsantoni Maria's avatar
    c4e20a21
    handle polyA processing in input preparation script · c4e20a21
    BIOPZ-Katsantoni Maria authored and Alex Kanitz's avatar Alex Kanitz committed 
    - 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
    c4e20a21
    History
    handle polyA processing in input preparation script
    BIOPZ-Katsantoni Maria authored and Alex Kanitz's avatar Alex Kanitz committed 
    - 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