Answers.Body: <p>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.</p>
  <p>&quot;No&quot; isn't completely correct: it'd be <em>possible</em> 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.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-08T02:21:10.283Z
Answers.LastActivityDate: 2020-07-08T02:21:10.283Z
Answers.UserDisplayName: gringer
Body: <p>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?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-07T22:25:55.207Z
Comments.Text: Hi @Samir ... you've got the files from here https://www.ncbi.nlm.nih.gov/geo/ cool, could you just fill in details about viewing and bigWig format for the rest of us?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-08T01:27:25.977Z
Comments.Text: 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.
Comments.UserDisplayName: Samir
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-08T11:29:22.433Z
Comments.Text: 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
Comments.UserDisplayName: StupidWolf
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-08T15:36:38.603Z
Comments.Text: Hi, this is the GEO accession: GSE102838
Comments.UserDisplayName: Samir
Tags: <rna-seq><rna><bigwig>
Title: RNA seq .counts.txt to bigwig conversion
ThreadText: # RNA seq .counts.txt to bigwig conversion
  
  (Asked by: username_0 on 2020-07-07)
  
  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?
  
  **Tags:** rna-seq, rna, bigwig
  
  > **Comments:**
  > **username_1**: Hi @username_0 ... you've got the files from here https://www.ncbi.nlm.nih.gov/geo/ cool, could you just fill in details about viewing and bigWig format for the rest of us?  
  > **username_0**: 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.  
  > **username_2**: 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  
  > **username_0**: Hi, this is the GEO accession: GSE102838  
  
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  ## 1 answers
  
  ### Answer by username_3 on 2020-07-08. Score: 1
  
  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.
  
  
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