0
$\begingroup$

I've downloaded neuronal RNA seq data from GEO. The files are in .counts.txt format. Could I convert them to bigwig? If so, how?

$\endgroup$
4
  • 1
    $\begingroup$ Hi @Samir ... you've got the files from here ncbi.nlm.nih.gov/geo cool, could you just fill in details about viewing and bigWig format for the rest of us? $\endgroup$
    – M__
    Jul 7, 2020 at 22:25
  • 1
    $\begingroup$ Hi Michael. I want to load RNA seq data into HiGlass, a browser that I use to look at my HiC data. I have previously loaded RNA seq bigWig files into HiGlass. I just don't know if there is a way to load the text file format into HiGlass, so I wanted to know if I can convert the format to bigWig. $\endgroup$
    – Samir
    Jul 8, 2020 at 1:27
  • $\begingroup$ can you provide the GEO accession ? Sometimes they do provide bigwig but i suspect it's not very useful for RNAseq unless there's something specific u need $\endgroup$
    – StupidWolf
    Jul 8, 2020 at 11:29
  • $\begingroup$ Hi, this is the GEO accession: GSE102838 $\endgroup$
    – Samir
    Jul 8, 2020 at 15:36

1 Answer 1

1
$\begingroup$

No, count-level data doesn't have the base-level resolution that is required in order to be usefully visualised on a genome browser. You need a BAM file (or raw FASTQ files that can be used to generate a BAM file) in order to do that.

"No" isn't completely correct: it'd be possible to take gene counts and information about gene annotation boundaries to shoehorn them into a BedGraph / BigWig file, but whatever comes out the other end of that isn't going to be a good representation of reality.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.