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  • noiseq, where to download hg19 gene feature length?

    Dear all
    This might be a very native question but I really want to find out the answer ASAP.
    I am trying to use Noiseq tool on human genomic data and would like to supply the function with the file of gene feature length. (the initial hg19 gtf file I downloaded was from USCS) and the gene counts are in gene symbol format. i.e.
    "A1BG"
    "A1BG-AS1"
    "A1CF"

    Does anyone which site I can use to directly download the gene length table, such as
    Gene-ID Length
    "A1BG" 2543
    "A1BG-AS1" 248
    "A1CF" 669

    *I fabricated the length in the example just to show what format I am looking for.
    Also, does any noiseq user believe the gene length information is really important?

    Thanks a lot

  • #2
    You should be able to use "Table Browser" from UCSC or BioMart tool from Ensembl for getting this info. See example filter below. I am using "Uniprot GeneName" filter for this example. Substitute with the appropriate Gene Name filter you are looking for.



    You will need to subtract the "start" value from the "end" to get the length. You can easily export the table in "csv" format from BioMart and then edit in excel.

    Comment


    • #3
      Originally posted by GenoMax View Post
      You should be able to use "Table Browser" from UCSC or BioMart tool from Ensembl for getting this info. See example filter below. I am using "Uniprot GeneName" filter for this example. Substitute with the appropriate Gene Name filter you are looking for.
      yeah, thanks. I got nearly all my necessary features.

      Originally posted by GenoMax View Post
      You will need to subtract the "start" value from the "end" to get the length. You can easily export the table in "csv" format from BioMart and then edit in excel.
      As for "feature length", I am a little confused. Your suggestion above is ok for "gene feature length", but what about "protein_coding feature" or "transcript feature"? Your method will include length of introns. In a rna-seq analysis with NOISeq, the feature length we provided doesn't mean the length of corresponding transcript? And if I want the transcript length feature, how do I get the file of length feature for all transcripts?
      Last edited by eastasiasnow; 01-22-2014, 02:01 AM. Reason: mis-meaning in my sencentes

      Comment


      • #4
        Under the attributes filter (instead of the gene start/end as in example above), under "sequence", you can either select "cDNA sequence" (to get all transcripts) or "exon sequence" (to get all possible exons) for a specific gene. Depending on the feature you choose "CDS length" (Exon features) or "Transcript Start/End" (Transcript Information) should give you the length in the FASTA headers. You will have to parse those out by a simple "grep".

        OR

        Under the attributes --> select "Features" and then the following.
        Attached Files
        Last edited by GenoMax; 01-22-2014, 04:26 AM.

        Comment


        • #5
          @GenoMax
          Thanks, This should work. I found a script from this post:
          Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


          I made small changes to that awk script for applying it to the latest ensemble gff file of zea mays AGPv3.21, it works fine so far, and I can get the length of all transcrits.
          Last edited by eastasiasnow; 01-22-2014, 06:54 AM. Reason: grammer errors

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