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cpreid2 / gdc-rnaseq-tool

Tool to download/merge RNASeq data from the GDC Portal in matrices identified by TCGA barcode
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comments #3

Closed hsahni closed 6 years ago

hsahni commented 6 years ago

Hi Colins, looks really good!. Some feedback

  1. I think we need to describe the problem domain as in what problem this tool is helping solve and how is it doing it (uses manifest to download the files, extracts xyz from downloaded files and generates a tabular result of adc etc.

  2. Further describe the input RNA/MiRNA expression data

    • Does the input need to be only Transcriptome Profiling,isoform Expression Quantification miRNA-Seq TSV files ?
    • Does it work for all projects or just TCGA ?
    • Do the files need to be open access only?
    • Works on GDC harmonized Portal files & legacy files? or just harmonized portal files.
    • Perhaps add a link to an example gdc query

  3. Description of what the values represent within each of the output files would be very helpful

    --------------
Creating merged HTSeq - Counts File... ( Merged_Counts.tsv )
--------------
Creating merged HTSeq - FPKM-UQ File... ( Merged_FPKM-UQ.tsv )
--------------
Creating merged HTSeq - FPKM File... ( Merged_FPKM.tsv )
--------------
Creating merged miRNASeq Counts File... ( Merged_miRNA_Counts.tsv )
Creating merged miRNASeq rpmm File... ( Merged_miRNA_rpmm.tsv )

  4. I have been using python 2.7 so had to install python 3 from scratch (Installed python36.32) so I had to also install requests package

    C:\Python36-32>py gdc-rnaseq-tool.py -h
Traceback (most recent call last):
File "gdc-rnaseq-tool.py", line 1, in <module>
import requests
ModuleNotFoundError: No module named 'requests

  5. BTW (on windows) I generally use the following to install packages py -m pip install <<package>>

cpreid2 commented 6 years ago

@hsahni Thanks for the great feedback. I've updated the Readme with some more detail.