RNA-seq gene list - HOMER Gene based analysis
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3.9 years ago
G.Car ▴ 20

I have received an excel RNA-seq gene list of differentially expressed genes. I would like to use Homer's Gene based analysis to look upstream of the TSS of these genes and find potential motifs of transcription factors for hypothesis generation, which I can then test in the wet lab.

I've got homer set up and I'm using the command:

findMotifs.pl agmo_id.xlsx mouse RNA_seq/ -start -400 -end 100 -len 8,10 -p 4

However, homer spits back that it is unable to open the file. I tried saving it as a tab-delimited plain text file, but I have the same response.

The file contains the accession numbers and the log2 fold change of the genes. The accession numbers are ensembl.

What file format should I be saving it as? I've tried tab delimited, comma delimited and basic excel files, but none seem to work.

Thanks

RNA-Seq homer • 1.2k views
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Entering edit mode
3 days ago
bkleiboeker ▴ 20

Replying for anyone in the future:

"If you're having trouble with the program, 9 out of 10 times it is due to an incorrectly formatted input file. If using EXCEL (especially on the Mac), make sure to save input files as 'Text (Windows)'" (from http://homer.ucsd.edu/homer/microarray/index.html)

For me on OS Catalina (10.15.2) I have been saving (from .csv) as "MS-DOS formatted text (.txt)" with the first column as ENTREZIDs and that file reads just fine into findMotifs.pl function

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