HOMER tss command not working

Question

[carlee.bettler]

Hi,

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!

Answer 1

[Arup Ghosh]

Seems like the mm9 TSS(mm9.tss) file is not present in Homer data folder. Reinstall the genome files using configureHomer.pl -install mm9 command. To get a list of available datasets and tools use configureHomer.pl -list command.