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cinquin / MEME

MEME motif-based sequence analysis tools (http://meme-suite.org), with FreeBSD tweaks
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FIMO output gff file not being uploaded to UCSC #6

Open atasub opened 2 years ago

atasub commented 2 years ago

Hi,

I am not able to upload the FIMO output gff file to the UCSC. The file looks like such:

gff-version 3

clu_929_NA fimo nucleotide_motif 24544 24553 59.5 + . Name=100_clu_929_NA+;Alias=10;ID=100-10-1-clu_929_NA;pvalue=1.11e-06;qvalue=0.297;sequence=TCTTCTCTTC; clu_929_NA fimo nucleotide_motif 24796 24805 49.2 - . Name=100_clu_929_NA-;Alias=10;ID=100-10-2-clu_929_NA;pvalue=1.2e-05;qvalue=0.362;sequence=TCTTCTCTGC;

I think the problem is related to the first column, which is expected to be "chrN" kind. I tried to run with the '--parse-genomic-coord' option too. However, it did not help.

Could you please help?