CrossMap issues changing genome version
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
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?
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