Question: HOMER tss command not working
0
gravatar for carlee.bettler
13 months ago by
carlee.bettler10 wrote:

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!

tss chip-seq homer • 560 views
ADD COMMENTlink modified 13 months ago by Arup Ghosh2.7k • written 13 months ago by carlee.bettler10
2
gravatar for Arup Ghosh
13 months ago by
Arup Ghosh2.7k
India
Arup Ghosh2.7k wrote:

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.

ADD COMMENTlink written 13 months ago by Arup Ghosh2.7k
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