How to reproduce TCGA rsem values from firebrowse

Question

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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?

Answer 1

[GenoMax]

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

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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?

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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