CrossMap issues changing genome version

CrossMap issues changing genome version


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

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?



software error


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