Execution Workflow: TAPAS

[ninsch3000]

WHAT

Write execution workflow for TAPAS. 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
• [x] Input: .bam or .fastq from test_data
• [x] 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.

[SamBryce-Smith]

Hey @yoseopyoon

Just wanted to check if you're still going to be able to contribute to this workflow? Absolutely not a problem if not (though would be great if you still want to help out!), it's mainly so the rest of the group know what still needs to be done.

Also, if you've managed to make any progress so far it would be great to see any of your code pushed, even if it's still a work in progress! Most of all you'll get credit for your work but then others can join in too without starting from scratch.

Thanks :)

[yoseopyoon]

Hi Sam,

Thanks for contacting me. Since I am an RNA biologist with poor background in bioinformatics, I think it would be better to have someone else to continue work on this issue. However, I am willing to contribute to other areas such as manuscript, literature search etc.

I don’t have any code to push; below is what I tried during APAeval: • I installed TAPAS, figured out how to run it using our small sample data set • Troubleshooted converting our test annotation file to refFlat and found it requires “NM_” identifier to be run by the command. Etc. • I updated TAPAS section of methods summary spreadsheet and also uploaded TAPAS results from our small test data • Submitted feedback about the method

Thank you !!

Best,

Yoseop

Yoseop Yoon, Ph.D. Postdoctoral Scholar Shi Lab Department of Microbiology & Molecular Genetics School of Medicine University of California, Irvine

On Jul 2, 2021, at 7:26 AM, SamBryce-Smith @.***> wrote:

Hey @yoseopyoon https://github.com/yoseopyoon Just wanted to check if you're still going to be able to contribute to this workflow? Absolutely not a problem if not (though would be great if you still want to help out!), it's mainly so the rest of the group know what still needs to be done.

Also, if you've managed to make any progress so far it would be great to see any of your code pushed, even if it's still a work in progress! Most of all you'll get credit for your work but then others can join in too without starting from scratch.

Thanks :)

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[yuukiiwa]

Hi @SamBryce-Smith, I will be taking over the TAPAS execution workflow. Thank you so much for all your effort, @yoseopyoon!

[SamBryce-Smith]

Update on the progress of TAPAS execution workflow

@yuukiiwa implemented a nextflow pipeline on branch TAPAS. When trying to run with test data (i.e. much smaller than a typical dataset), the workflow exited with a 137 error code (out of memory error code). See screenshot below & attached nextflow.log for this run.

nextflow.log

This workflow is currently on hold whilst we focus on other aspects of the challenge, but we may return to this to try and debug (other APA tools/papers have managed to get it running).

[SamBryce-Smith]

I spotted on branch TAPAS that the read-length parameter (-l) was missing the from TAPAS APA_sites_detection call.

@yuukiiwa addressed this (3d9f687e159a63a83ebc4e000b3405f3213cc502) and re-ran the workflow with a 12MB BAM file for testing. The workflow completed successfully in 8 hours (!).

Execution workflows are currently a low priority right now, but it does seem possible to get TAPAS to generate APAeval-compliant outputs (although the scalability of the tool to large/full-size datasets is a concern...)

[faricazjj]

@yuukiiwa @SamBryce-Smith thank you guys for all the work!! Are we planning to create a PR for TAPAS branch to be merged to main?