missing pval_nominal_threshold column in output cis_qtl.txt file

[jeoneunyoung]

We are having such a great time using tensorqtl. Thanks for the wonderful tool.

I am currently having trouble with missing pval_nominal_threshold column in my output cis_qtl.txt file when running in --mode cis. Other columns are appearing just fine, but the pval_nominal_threshold column.

If I run with the same --mode cis command with different expression bed file, I get the pval_nominal_threshold column.

Do you possibly know why this is happening?

Sincerely,

Leah

[jeoneunyoung]

Nevermind :) There were no signals below qval 0.05!

[CuteGold0407]

hi，i met the same issue(;_;)，when i run the same code on different phenotype files, like chr2 and chr3, the outfile of chr3 have the pval_nominal_threshold column, but chr2 didn't. do you know how to fix that?

[francois-a]

If you're running tensorqtl on subsets of phenotypes, you'll need to combine the outputs first, and then compute q-values on the combined output, using post.calculate_qvalues. See here for example.