reskejak / ATAC-seq

Basic workflow for ATAC-seq analysis

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Error in csaw_workflow: Error in (function (classes, fdef, mtable) (csaw_workflow.R#116): unable to find an inherited method for function ‘seqinfo’ for signature ‘"NULL"’ #15

Open prmunn opened 10 months ago

prmunn commented 10 months ago

I get this error when running:

count BAM reads in, e.g. 300 bp windows

counts <- windowCounts(pe.bams, width=300, param=param) # set width as desired from the fragment length distribution analyses

in the csaw_workflow.R script. I'm running R 4.3.0 and have updated all of my Bioconductor packages. Any idea what's causing this?

mglgc commented 2 months ago

Hi. If you have fixed this issue, please could you be so kind for sharing? I'm facing to this issue with no success. Thank you so much.

I get this error when running:

count BAM reads in, e.g. 300 bp windows

counts <- windowCounts(pe.bams, width=300, param=param) # set width as desired from the fragment length distribution analyses

in the csaw_workflow.R script. I'm running R 4.3.0 and have updated all of my Bioconductor packages. Any idea what's causing this?

prmunn commented 1 month ago

@mglgc Sorry for the delay in getting back to you. I was never able to resolve this issue - hoping that the package authors come up with an answer.