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nunofonseca / irap

integrated RNA-seq Analysis Pipeline
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more guideline for Atlas SOP #35

Closed wangyugui closed 6 years ago

wangyugui commented 6 years ago

Hi @nunofonseca

We need more guideline for Atlas SOP to get the same result like Expression Atlas.

Result sample: https://www.ebi.ac.uk/gxa/experiments/E-MTAB-2690/Downloads

Question1: How to get both TPM and FPKM Expression values across all genes? "sop=atlas" does not work as expected.

Question2: Can we run iRAP without DE when we get these TPM and FPKM Expression values ?

I used the version irap-v0.8.5p4 but failed to the right way to do these.

Best Regards

nunofonseca commented 6 years ago

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.

wangyugui commented 6 years ago

'irap_single_lib' works well.

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