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Execution Workflow: DaPars2 #32

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4 of 8 tasks
ninsch3000 opened this issue May 25, 2021 · 0 comments · Fixed by #193
Closed
4 of 8 tasks

Execution Workflow: DaPars2 #32

ninsch3000 opened this issue May 25, 2021 · 0 comments · Fixed by #193

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@ninsch3000
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ninsch3000 commented May 25, 2021

WHAT

Write execution workflow for DaPars2. Use the provided small files for testing (running the workflow on real data is a different issue).

CHECKLIST

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.

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