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...
- If I use following command to convert
CrossMap.py bam ./mm10ToMm9.over.chain.gz ./accepted_hits.bam ./accepted_hits_mod
I get the
UnboundLocalError: local variable error.
- And if I use the command to convert
bedfile, 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?