Question: How to reproduce TCGA rsem values from firebrowse
0
gravatar for -_-
14 months ago by
-_-720
Canada
-_-720 wrote:

I would like to apply TCGA's mRNA quantification pipeline to other samples, but I couldn't find detailed documentation about how their expression values are quantified? Here is what I know so far:

rsem is used for expression quantification.

What about the aligner (together with the parameters used), reference file, and any kind of preprocessing (e.g. FastQC?)

Does anyone have a link to more details?

expression rsem tcga • 753 views
ADD COMMENTlink modified 14 months ago by genomax59k • written 14 months ago by -_-720
2
gravatar for genomax
14 months ago by
genomax59k
United States
genomax59k wrote:

See my answer in this thread to get the details of processing pipelines used at UNC and GDC: TCGA data, relationship between different sources

ADD COMMENTlink modified 14 months ago • written 14 months ago by genomax59k
1

Hi @genomax, do you happen to know if the same pipeline has been applied to obtain expression values of samples any other cancer projects (e.g. CCLE), please?

ADD REPLYlink written 14 months ago by -_-720

Thanks! Based on your link, I found a couple of very useful links:

  1. A writeup of basically exactly the question I am facing: http://bsbludwig.com/post/94066296740/what-do-tcgas-rnaseq-files-actually-show#disqus_thread
  2. More details about the UNC pipeline using RSEM: https://webshare.bioinf.unc.edu/public/mRNAseq_TCGA/UNC_mRNAseq_summary.pdf
ADD REPLYlink written 14 months ago by -_-720
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