TSS file format - loadPromoters.pl in Homer

Hi all, I'd like to load TSS sites to Homer, however I don't know what format loadPromoters.pl accept. Here is appropriate page from manual, but it is not clear in this respect.

I have gff file with experimentally determined TSS.

Does anybody used this command? What is your experiences?

tss homer

• 1,119 views • link

written 5.3 years ago by boczniak767

0 answers

No answers yet.

More posts like this

Discrepancies Between GEO Page and its article - Seeking Clarification
written 2.8 years ago by AlexStar •

How should I interpret the information from the article GSE145281? On the GEO page, it mentions bladder cancer. However, the article itself specifies that the …
Extract transcript fasta using gff
written 5.2 years ago by boczniak767

Hi, is there simple way to extract `fasta` sequences of transcripts using genome `fasta` and `gff`? I came across [gffread][1] which propose command `gffread -w …
HOMER tss command not working
written 7.0 years ago by 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 …
What is the GMAP GFF3 score?
written 7.3 years ago by James Reeve

I'm looking into filtering a GFF3 file I generated from GMAP. Looking online it's clear that there isn't a universal way to filter GFF3s, but …
Editing/Updating Homer Motifs
written 7.9 years ago by shankasal •

I have a few questions regarding the motif finding function of HOMER. 1) I'm trying to run an update on the motifs with updateMotifFiles.pl but …
List of TSS from GTF file
written 8.3 years ago by Roman Hillje •

Hi, I'd like to create lists of transcription start sites based on the GTF files of the multiple annotation sets we have in our group. …
Setting/finding the log odds detection threshold in custom homer PWMs
written 8.4 years ago by endrebak

I want to convert the JASPAR pwms to homer format: http://jaspar.genereg.net/downloads/ It seems like the JASPAR files in the transfac format are pretty close: AC …
Aligning de-novo assembly to reference strain genome
written 9.5 years ago by aindap

Dear Biostars Community - I generated a de-novo assembly of my viral strain. I wanted to analyze differences of my denovo result to a reference …
CNV analysis using the ExomeDepth R Package
written 10.6 years ago by cafelumiere12

Hi all, I'm looking into using exomeDepth R package for CNV analysis; however, I have a couple questions from reading the manual (https://cran.r-project.org/web/packages/ExomeDepth/vignettes/ExomeDepth-vignette.pdf) regarding building …
Given gene ID and genomic coordinates, how can I create a GFF formatted file?
written 12.1 years ago by Jason

I have downloaded a list of coordinates of yeast genes from [Xu et al., 2009][1] (see table S3). Unfortunately its current format is not a …