Question: CrossMap issues changing genome version
gravatar for Satyajeet Khare
2.7 years ago by
Satyajeet Khare1.3k
Pune, India
Satyajeet Khare1.3k wrote:

I installed CrossMap for conversion of bam, bed, gtf files from one version to another. I use GENCODE so I need to make the files compatible with UCSC browser. I am running into two issues with this tool...

  1. If I use following command to convert bam file bam ./mm10ToMm9.over.chain.gz ./accepted_hits.bam ./accepted_hits_mod

I get the UnboundLocalError: local variable error.

  1. And if I use the command to convert gtf or bed file, the command runs without error. The out file looks fine as it loses the GL ids from GENCODE. But if I load the file on UCSC, I see this error...

Error File 'merged_mod' - GFF/GTF group TCONS_00124661 on chrY_random+, this line is on chrY_random-, all group members must be on same seq and strand

Can anyone please help me out?

ADD COMMENTlink written 2.7 years ago by Satyajeet Khare1.3k
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