Question: CAGEFightR to get CTSS from CAGE error
0
gravatar for bharata1803
18 months ago by
bharata1803450
Japan
bharata1803450 wrote:

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 • 539 views
ADD COMMENTlink modified 4 months ago by bioinfo0 • written 18 months ago by bharata1803450

I have the same issue, anyone has a solution?

ADD REPLYlink written 8 months ago by jun.xu0

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

ADD REPLYlink written 4 months ago by bioinfo0
0
gravatar for kevinmarco.menden
5 months ago by
kevinmarco.menden0 wrote:

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!

ADD COMMENTlink written 5 months ago by kevinmarco.menden0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2087 users visited in the last hour