Help with an error with Homer

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15 months ago

Chris ▴ 340

Hi all,

I looked for this error on the Internet, but still don't know why. Would you please have a suggestion? Thank you so much!

findMotifsGenome.pl homer_format hg38 MotifOutput/ -size 200 -mask -len 8 -preparsedDir preparsed_dir

I got these files in the output folder but the file homerMotifs.all.motifs is nothing:

hg38r.200.cgbins hg38r.200.cgfreq hg38r.200.gcbins hg38r.200.pos hg38r.200.seq 0.200174538725154.motif.tmp

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Homer • 698 views

ADD COMMENT • link 15 months ago by Chris ▴ 340

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Is homer_format a BED file?

ADD REPLY • link 15 months ago by ATpoint 85k

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I converted bed to Homer format. Let me try with bed file. I still got that error but this time I even don't have temporary files.
Update: the reason of error is my bed file doesn't have chr prefix. However, my output file has RNA motif but not DNA eventhought my input is bulk ATAC-seq. Would you please have a suggestion?

ADD REPLY • link 15 months ago by Chris ▴ 340

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