search

kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
BSD 3-Clause "New" or "Revised" License
159 stars 81 forks source link

which files created by this pipeline can be used for homer to find motifs? #131

Closed llz-hiv closed 6 years ago

llz-hiv commented 6 years ago

There are 3 basic ways to run HOMER - with FASTA files, with Gene Identifiers, or from Genomic Positions. Can narrow peak files be directly used for Homer to find motifs?

Thanks

akundaje commented 6 years ago

NarrowPeak files are just BED files with more columns for additional information. If you extract the first 3 columns from the narrowPeak file, that will provide you the peak boundary coordinates. You should be able to feed that in any motif discovery method in whatever format they expect.