iRAP pipeline for EMBL-EBI Expression Atlas

[lissur]

Dear Nuno,

Is it possible to find all iRAP pipeline commands used to process a specific dataset in the EMBL-EBI Expression Atlas? If it is, where I can get this information?

Thank you,

Lissur.

[nunofonseca]

Dear Lissur,

You may enable the SOP used in Expression Atlas for bulk RNA-seq by adding sop=atlas to irap, either in the conf file or as an argument. All commands executed will be printed to the terminal. More details can be found in https://academic.oup.com/bioinformatics/article/33/14/2218/3078600.

Note that Expression Atlas further normalizes the expression values after getting the counts/tpms/fpkms.

Hope that this helps. Cheers.