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.

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:

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: