Software for motif discovery and next-gen sequencing analysis
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.bedThis 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:
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: