Execution Workflow: PAQR

[ninsch3000]

WHAT

Write execution workflow for PAQR. Use the provided small files for testing (running the workflow on real data is a different issue).

CHECKLIST

• [ ] Use snakemake template or nextflow template to create your workflow.
• [ ] Comment your code
• [ ] Run individual rules/processes in either conda envs or docker/singularity containers for reproducibility
• [ ] Input: .bam or .fastq from test_data
• [ ] Give feedback about the method

OUTPUTS (see specification):

• [ ] ~Output: Adhere to output specification for Identification challenge~ No identification

• [ ] Output: Adhere to output specification for quantification challenge

  This BED file contains positions of unique poly(A) sites with TPM values for each identified site in the score column.

  chrom - the name of the chromosome chromStart - the starting position of the feature in the chromosome chromEnd - the ending position of the feature in the chromosome; as identified PAS are single-nucleotide, the ending position is the same as starting position name - defines the name of the identified poly(A) site score - TPM value for the identified site strand - defines the strand; either "." (=no strand) or "+" or "-".

• [ ] Output: Adhere to output specification for differential usage challenge

  This TSV file contains two columns:

  • gene ID
  • significance of differential PAS usage

  Column names should not be added to the file.

[ninsch3000]

Labelled "low priority" and "blocked" because we're waiting for an update of PAQR's github repo, which is not easily usable at the moment.