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CAGEFightR to get CTSS from CAGE error

Hello,

So, I got bam files from CAGEseq experiment from FANTOM5. I realigned it to Ensembl GRCh 38 90 using bwa and then extract the bigwig file using deeptools bamCoverage.

Then I am trying to get the CTSS using CAGEFightR from the bigwig files (plus and minus strand) I have generated.

Using the quantifyCTSSs from CAGEFightR function, I got error "Error in asMethod(object): all the ranges in the object to coerce to GPos must have a width of 1"

What is wrong with my method?

cage-seq bioconductor
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updated by bioinfo • bioinfo • written by bharata1803 bharata1803

I have the same issue, anyone has a solution?

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written by jun.xu • jun.xu

Hi

did you solve this problem

I got error "Error in asMethod(object): all the ranges in the object to coerce to GPos must have a width of 1" I am having the same one

thanks

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written by bioinfo • bioinfo

1 answer

Hi,

I had a similar issue, as well as others. You might want to check out the CAGEfightR issues on the GitHub page: https://github.com/MalteThodberg/CAGEfightR/issues/1

There are some workarounds - mostly for the case where you already have CTSS files and no BigWigs. You can then use some R package (as a workaround) to generate BigWig files.

Hope that helps!

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written by kevinmarco.menden • kevinmarco.menden

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