search

nunofonseca / irap

integrated RNA-seq Analysis Pipeline
GNU General Public License v3.0
82 stars 33 forks source link

iRAP pipeline for EMBL-EBI Expression Atlas #107

Open lissur opened 4 years ago

lissur commented 4 years ago

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 commented 4 years ago

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.