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?
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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__ ♦Commented Jul 7, 2020 at 22:25
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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. $\endgroup$– SamirCommented Jul 8, 2020 at 1:27
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$\begingroup$ 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 $\endgroup$– StupidWolfCommented Jul 8, 2020 at 11:29
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$\begingroup$ Hi, this is the GEO accession: GSE102838 $\endgroup$– SamirCommented Jul 8, 2020 at 15:36
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1 Answer
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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.
