Question: How to reproduce TCGA rsem values from firebrowse
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gravatar for -_-
10 months ago by
-_-640
Canada
-_-640 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 • 544 views
ADD COMMENTlink modified 10 months ago by genomax54k • written 10 months ago by -_-640
2
gravatar for genomax
10 months ago by
genomax54k
United States
genomax54k 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 10 months ago • written 10 months ago by genomax54k

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 10 months ago by -_-640

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 10 months ago by -_-640
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