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How to reproduce TCGA rsem values from firebrowse

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?

tcga expression rsem
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updated by GenoMax GenoMax • written by -_- -_-

1 answer

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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written by GenoMax GenoMax

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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written by -_- -_-

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