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ngsplot - how to plot enrichment across TSSs of a list of genes instead of all TSSs

Hi, I'm a frequent user of ngsplot to plot enrichment of my chip-seq datasets across a given list of regions (bed file containing peaks). However, I am now trying to show this enrichment at the TSSs of a specific list of genes but I always get the same output even when I change the list itself. Thus, ngsplot is outputing enrichment across all TSSs. The command I use is:

ngs.plot.r -G mm9 -R tss -C config.txt -O outputfile-name -E Text-file-with-Ensembl-list-of-genes

My configuration file contains:

bam1.bam -1 “name1” bam2.bam -1 “name2”

I have used ngplot for this purpose in the past successfully, but cannot remember exactly how I did so. I've spent the last 2 days searching for an answer, so if there is a hidden webpage out there please point the way. Otherwise, could someone offer their insights? Thank you!

chip-seq
• 4,015 views • link
written by Sadia • Sadia

2 answers

If you want to specify the gene list as "genome", use "-1".

Use TAB to separate the three columns: coverage file<tab>gene list<tab>title

"title" will be shown in the figure's legend.

hesc.H3k4me3.rmdup.sort.bam high_expressed_genes.txt "High"

hesc.H3k4me3.rmdup.sort.bam medium_expressed_genes.txt "Med"

hesc.H3k4me3.rmdup.sort.bam low_expressed_genes.txt "Low"

I found this in the ngsplot manual, hope it can help you.

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written by ghostforever.shi • ghostforever.shi

Thanks for your reply. I had been doing what you suggested, but I thought I would give it another shot, and it seems to be working now for some reason, but I'll take it :)

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written by Sadia • Sadia

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