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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Indicate which analyses are part of manuscript #1290

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

This PR addresses Issue #1287 and adds a column to analyses/README.md to indicate if the analysis module is part of the manuscript with Yes or No. Small phrasing changes were also made.

For reviewers: there are two modules I wasn't sure about (either because it's not decided yet or it wasn't clear to me), and these currently are marked "UNKNOWN."

jharenza commented 2 years ago

rna-seq-composition

This is not currently in the manuscript

sample-distribution-analysis

I think this was subsumed by your plots of sample dist/seq strategy

jharenza commented 2 years ago

Just double checked this in the manuscript repo. We had added MENDQC in our quality control section, though we do not have any cutoffs for use/not use of data:

https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/master/content/06.methods.md#quality-control-of-sequencing-data

MEND QC [42] was performed on aligned RNA-Seq reads using this workflow to identify mapped exonic non-duplicate reads.

So, should we include that here or remove from the QC section?

jaclyn-taroni commented 2 years ago

I would remove it from the QC section if we did not use it and leave this as is