Execution workflow: AltTSSPAS

[faricazjj]

Child issues

Proof of concept: https://github.com/iRNA-COSI/APAeval/issues/276 Implementation: https://github.com/iRNA-COSI/APAeval/issues/272 Testing & review: https://github.com/iRNA-COSI/APAeval/issues/274

WHAT

Write execution workflow for InPAS. 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

  This BED file contains single-nucleotide position of poly(A) sites identified by the tool. Fields:

  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 - not used, leave as "." strand - defines the strand; either "." (=no strand) or "+" or "-".

• [ ] 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.

[faricazjj]

As commented in the proof of concept issue https://github.com/iRNA-COSI/APAeval/issues/276, the paper for this tool doesn't seem to be available. We emailed the author for confirmation on paper availability (preprint or published), which we require for a tool to be included in our evaluation.

Will close this issue and the child issues once the author confirms or if the author doesn't respond by June 30.

[faricazjj]

Got a confirmation today (June 27, 2022) from the author that the tool isn't ready for evaluation. Closing all issues related to AltTSSPAS.

@SamBryce-Smith @yuukiiwa @mrgazzara