Question: CrossMap issues changing genome version
gravatar for Satyajeet Khare
4.4 years ago by
Satyajeet Khare1.6k
Pune, India
Satyajeet Khare1.6k 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 4.4 years ago by Satyajeet Khare1.6k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2641 users visited in the last hour