CAGEFightR to get CTSS from CAGE error

Question

[bharata1803]

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?

[jun.xu]

I have the same issue, anyone has a solution?

[bioinfo]

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

Answer 1

[kevinmarco.menden]

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!