HOMER
Software for motif discovery and next-gen sequencing analysis
Miscellaneous Tools for Sharing Data
HOMER contains several utility programs for changing file formats and performing tasks that you may find useful from time to time. Below are a list of programs that may come in handy.Outputing Tag Directory as a BED file (tagDir2bed.pl):
This is useful when you want to
share your sequencing with others as BED format is about the most
general format there is out there.
tagDir2bed.pl
<tag directory> > output.alignment.file.bed
i.e. tagDir2bed.pl Macrophage-PU.1-ChipSeq/ > mac.pu1.bed
This will produce a large BED file that can be used to import the data
to other programs.i.e. tagDir2bed.pl Macrophage-PU.1-ChipSeq/ > mac.pu1.bed
Coverting between HOMER peak and BED file formats (pos2bed.pl / bed2pos.pl):
Want to load HOMER peaks into the
genome browser? Or use them with other software?
Covert a HOMER peak/position file to a BED file:
Covert a BED file to a HOMER peak/position file:
Covert a HOMER peak/position file to a BED file:
pos2bed.pl
<peak file> > output.bed
Covert a BED file to a HOMER peak/position file:
bed2pos.pl
<BED file> > output.peakfile.txt
Can't figure something out? Questions, comments, concerns, or other feedback:
cbenner@salk.edu