Hello
I'm trying to plot the coverage of a bam file from a ChIP-seq experiment via NGSplot and I get the following error:
Configuring variables...Error in CheckRegionAllowed(reg2plot, default.tbl) :
Unknown region specified. Must be one of: bed
Execution halted
This is the command I'm using:
ngs.plot.r -G mm10 -R tss -C myfile.bam -O mybamfile.ngs
If I change the -R from "tss" to "bed" and specify a bed file I get from the PeakCaller software, it works just fine. However, I want it to take into consideration only the bam file
Any ideas why I'm getting this error message?
Thanks
•
written
by
Constantine
The problem could be that your region's file does not end in .bed?
Otherwise, I suggest you to use deepTools instead (note: I am part of the developing team). Simply:
pip install deepTools
bamCoverage -b myfile.bam -o myfile.bw
computeMatrix -R tss -S myfile.bw -o matrix
profile -m matrix -o profile.pdf
Also, once you have a matrix you can plot a heatmap and add some clustering:
heatmapper -m matrix --kmeans 2 -o heatmap.png
You can take a look at the documentation (https://github.com/fidelram/deepTools/wiki) for more information.
I'm mainly using deeptools (prefer it better) ;)
Just wanted to also use NGS to see whether I'm getting the same output...Guess I'll have to stick with deeptools then
"computeMatrix: error: argument : invalid choice: 'tss' (choose from 'scale-regions', 'reference-point')" now this doesn't work .
But when i using the something like this
"computeMatrix scale-regions -S 10_S10_L002sorted_rem.bam.bw 11_S11_L002sorted_rem.bam.bw -R gencode.v21.annotation.bed --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -o matrix.mat.gz
"
It takes a lot of time but when i choose like chr21 this for my bed region it generates the matrix ...how to reduce the matrix generation time ?
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