error in index.genotype() function in sQTLseekeR

jmonlong / sQTLseekeR

R package to detect splicing QTLs (sQTLs)

http://big.crg.cat/computational_biology_of_rna_processing/sqtlseeker

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error in index.genotype() function in sQTLseekeR #11

Open tingqi opened 4 years ago

tingqi commented 4 years ago

Hi,

I was running sQTLseekeR and got an error message "[E::get_intv] Failed to parse TBX_GENERIC, was wrong -p [type] used? The offending line was: "chr start end snpId". It seems that there is some issue about this function "Rsamtools::indexTabix(file.final, format = "bed")". This error message seems to be the newly generated error. Previously, I also run sQTLseekeR using tested data and real data, and it works well. Could you please help have a check? Thank you.

Cheers, Ting

Yijun-Tian commented 3 years ago

I made some updates for the index.genotype.R file in the pull request. You can try adding a # to your genotype file and run this new index script. Rsamtools seems to be mad with the header line if without comment sign in the newest release. Let me know if this works for you.

chz31 commented 2 years ago

@Yijun-Tian I got the same error. Can you please let me know how to modify this sample file, like where to add '#"? Thanks!