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morrislab / qapa

RNA-seq Quantification of Alternative Polyadenylation
GNU General Public License v3.0
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Build library for rat #21

Closed jchariker closed 5 years ago

jchariker commented 5 years ago

Hi, I am following instructions to build a library for rat, and I am getting an error using the following command: qapa build -N --db Rn6_Ensembl_sorted.txt Rn6_Gencode.txt > output.utrs.bed

The error message is: [qapa] Error: Command was: bedtools groupby -o collapse,collapse,collapse,collapse -i /tmp/pybedtools.rq16ugfd.tmp -g 1,2,3,6,7,8,9 -delim | -c 4,5,10,11 Error message was:

***** ERROR: Requested column 4, but database file /tmp/pybedtools.rq16ugfd.tmp only has fields 1 - 0.

I attached the Ensembl and Gencode files. They appear similar to the example files you posted for human and mouse. Do you have any thoughts on what might be going wrong? Thanks for any help you can give me. Julia Rn6_Ensembl_sorted.txt Rn6_Gencode.txt

kcha commented 5 years ago

Hi Julia, thanks for your question and posting your files. Indeed there was a bug in handling Ensembl IDs for species other than human and mouse. I have pushed a fix which should resolve your issue now. Hope this helps! If not, feel free to reopen this issue.

jchariker commented 5 years ago

Thank you very much. It works beautifully now! Julia