mafsInRegion

[VandaGLovejoy]

Hi,

I’m trying to extract chr1:4,000,000–10,000,000 from the Ensembl EPO (release 112) MAFs, but mafsInRegion keeps producing an empty file—even though I can see blocks in that range inside the source MAFs.

printf "1\t4000000\t10000000\n" > region.bed

# Extract from all chr1 chunks into one MAF
mafsInRegion region.bed epo.4M_10M.maf 43_mammals.epo.1_*.maf.gz

s homo_sapiens.1 5687873 21179 + 248956422 ...

thank you!

[Luis Nassar]

Hello,

Could you send us a small portion of the file that reproduces the problem?

We suspect it is because the Ensembl file is not organized the way the utility expects. Another engineer proposes an external tool (https://jydu.github.io/maffilter/maffilter.html#OrderFilter) that may help, but we can't offer any support for that tool.

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Lou Nassar
UCSC Genomics Institute