How to convert BigWig file to GCT File?

Question

[NikhilP]

I have this bigwig file generated from RNA Seq analysis and I want to convert that file into GCT file. How can I convert that?

Is there any n number of steps or can I do it directly using any tool in python/linux?

Edit: - Raw reads were aligned to the hg38 genome using STAR aligner. Bigwig files were generated using deeptools bamCoverage version v3.5.0, command –normalizeUsing BPM--binsize 1. GCT: - a tab-delimited text file that contains gene expression data.

[Ram]

What is a GCT file? "this bigwig file generated from RNA Seq analysis" is extremely vague. How was it generated and what does it contain?

[bk11]

GCT is GenePattern Cell Trajectory?

[Ram]

Why are you asking me - I've already expressed that I do not know what a GCT file is. Also, it doesn't seem like a "tab delimited file with gene expression" is a GenePattern Cell Trajectory. It's probably just a random file extension that someone in OP's lab came up with.

EDIT: I was wrong, thank you GenoMax and bk11.

[GenoMax]

GCT files: https://www.genepattern.org/file-formats-guide#GCT

This line required to defeat biostars spam detection code.

[rfran010]

I am not familiar with tools to work with GCT files, but a quick search seems like these may have something helpful:

https://cloud.genepattern.org/

https://www.genepattern.org/file-formats-guide#_Creating_Input_Files_GCT

https://clue.io/connectopedia/gct_format

I imagine the direct conversion from bigwig to GCT isn't really done. You could use something like deeptools and a GTF file to aggregate values from the bigwig over genes. However, this would be probably be straying pretty far from best practices, but if this is really all you have access to and for some reason need to work with a GCT file, this may be one way to do it. Also, to emphasize, the count data you will get from the bigwigs wouldn't be the normal input info for a GCT file.

I imagine there may be a better way to accomplish your overarching goal.