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natsuhiko / rasqual

Robust Allele Specific Quantification and quality controL
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condition specific eQTLs #15

Closed gouthamatla closed 5 years ago

gouthamatla commented 5 years ago

Hi, I would like to know if there is any way to identify condition specific eQTLs with RASQUAL. I have two conditions from same samples. I am interested to see the eQTLs that are detected in one condition but not in other and vice-versa.

If not by RASQUAL, is there an easy way of doing it ? Any pointers would be very useful.

natsuhiko commented 5 years ago

Unfortunately, there is no function to properly perform conditional specific eQTL mapping with RASQUAL. You can only map eQTLs separately for those two conditions, and draw a threshold (e.g., FDR 10%) to classify a pair of eQTLs into shared, condition specific, or null for both conditions. I would recommend to use other approaches, such as MASHR, to perform a proper analysis for this purpose.

gouthamatla commented 5 years ago

Thanks,

I will check MASHR.