CrossMap issues changing genome version

Question

[Satyajeet Khare]

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

CrossMap.py 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?

[ellenbdrake30]

Hi Satyajeet - I see you ran into this issue several years ago. Did you ever find a solution? I am getting the same error after using CrossMap to convert from mm10 to mm9 when I upload the converted file into UCSC.