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  • Getting level of spliced genes from gff-file

    Hi,

    I have a list of genes and I want to check how many of them are spliced, i.e. have multiple exons. Many of these genes also exist in several isoforms, but I mostly just need to know if a gene is multi-exonic or not.

    Any tips on how to efficiently calculate this? I have used bedtools before, but cannot see that it can do this task for me. Maybe cufflinks is an alternative, but I am not familiar with everything it can do.

    Thanks,

    Jon

  • #2
    Presuming you have a GTF or GFF file, you can use the GenomicRanges package in R. Just load the GTF/GFF file into a GRanges object, split() by the gene name, reduce() that and then lapply() length(). Multiexonic genes will have lengths > 1 (the result of applying length() will be the number of exons).

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    • #3
      Thanks Devon,

      I struggle to understand how to split by the gene name, and also to understand exactly how the output of this contains (GRangesList?). Should I split using "ID" or "gene"? Do you mind showing me on this exctract from my gff3 file? Thanks a lot.

      Code:
      ##gff-version 3
      ###
      scis2053	noncoding	gene	27485	28677	.	-	.	ID=scign013105;Name=scign013105
      scis2053	noncoding	mRNA	27485	28677	5921	-	.	ID=scitn013105.1;Parent=scign013105;Name=scitn013105.1
      scis2053	noncoding	exon	27485	28677	.	-	.	Parent=scitn013105.1
      ###
      scis543	noncoding	gene	28381	29172	.	+	.	ID=scign020729;Name=scign020729
      scis543	noncoding	mRNA	28381	29172	3731	+	.	ID=scitn020729.1;Parent=scign020729;Name=scitn020729.1
      scis543	noncoding	exon	28381	29172	.	+	.	Parent=scitn020729.1
      ###
      scis396	noncoding	gene	286737	287339	.	-	.	ID=scign021128;Name=scign021128
      scis396	noncoding	mRNA	286737	287339	3015	-	.	ID=scitn021128.1;Parent=scign021128;Name=scitn021128.1
      scis396	noncoding	exon	286737	287339	.	-	.	Parent=scitn021128.1
      ###
      scis673	noncoding	gene	85677	115116	.	+	.	ID=scign002358;Name=scign002358
      scis673	noncoding	mRNA	113016	115116	6254	+	.	ID=scitn002358.1;Parent=scign002358;Name=scitn002358.1
      scis673	noncoding	exon	113016	113049	.	+	.	Parent=scitn002358.1
      scis673	noncoding	exon	113444	114538	.	+	.	Parent=scitn002358.1
      scis673	noncoding	exon	114973	115116	.	+	.	Parent=scitn002358.1
      scis673	noncoding	mRNA	85677	115099	3835	+	.	ID=scitn002358.2;Parent=scign002358;Name=scitn002358.2
      scis673	noncoding	exon	85677	85697	.	+	.	Parent=scitn002358.2
      scis673	noncoding	exon	113896	114538	.	+	.	Parent=scitn002358.2
      scis673	noncoding	exon	114973	115099	.	+	.	Parent=scitn002358.2

      Comment

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