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  • How to assemble mRNAs from gff file?

    I have a gff file of genes that exist in mulitple isoforms and often several versions of mRNAs. I want to assemble all the exons for each gene to represent the longest isoform. I have tried bedtools and gffread, but I only get the sequences for each feature in the gff file. Any tips on how to do this?

    Here's an example of my file:

    Code:
    ##gff-version 3
    ###
    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

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