more guideline for Atlas SOP about irap HOT 2 CLOSED

'irap_single_lib' works well.

and it seems that fpkms/TPM is generated by iRAP/DEXSeq.

from irap.

Hi,

Question1:
a) For details on how data is generated for Expression Atlas (per assay/sample) please take a look at https://doi.org/10.1093/bioinformatics/btx143 (there is a file with the commands).
b) if you use irap (instead of irap_single_lib) then to get TPM and FPKM you will have to run irap twice (the second time it will only compute the TPM or FPKM, whatever is missing). Something like:
irap conf=your_conf_file.conf sop=atlas quant_norm_method=fpkm
irap conf=your_conf_file.conf sop=atlas quant_norm_method=tpm
c) if you still don' t get the results that you expect, then please give an example of what you would expect versus what you get.

Regarding question 2:
To disable DE analysis set de_method=none in your .conf file.

Cheers.

from irap.