I'm new to working with HOMER and I'm trying to find binding at transcription start sites for mouse genome mm9 Chip-Seq data.
Based on following the HOMER online manual at this link: http://homer.ucsd.edu/homer/ngs/quantification.html, my command is this:
/HOMER/bin/annotatePeaks.pl sampleBed.bed tss mm9 -size -500,1000 > homerTestOutput.txt
However, this gives me the error:
Genome tss not found
Which I then tried installing with:
HOMER/.//configureHomer.pl -install tss
But that just gives me this error:
could not find package: "tss"
I'm pretty stuck here, any thoughts or help would be much appreciated! Thanks!