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