SYNOPSIS
gt csa [option ...] [GFF3_file]
DESCRIPTION
-join-length [value]
- set join length for the spliced alignment clustering (default: 300)
-v [yes|no]
- be verbose (default: no)
-o [filename]
- redirect output to specified file (default: undefined)
-gzip [yes|no]
- write gzip compressed output file (default: no)
-bzip2 [yes|no]
- write bzip2 compressed output file (default: no)
-force [yes|no]
- force writing to output file (default: no)
-help
- display help and exit
-version
- display version information and exit
EXAMPLE:
Let's assume we have a GFF3 file csa_example_spliced_alignments.gff3 containing the following four overlapping spliced alignments (represented as genes with exons as children):
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##gff-version 3 ##sequence-region seq 1 290 seq . gene 1 209 . + . ID=gene1 seq . exon 1 90 . + . Parent=gene1 seq . exon 110 190 . + . Parent=gene1 seq . exon 201 209 . + . Parent=gene1 ### seq . gene 1 290 . + . ID=gene2 seq . exon 1 90 . + . Parent=gene2 seq . exon 101 190 . + . Parent=gene2 seq . exon 201 290 . + . Parent=gene2 ### seq . gene 10 290 . + . ID=gene3 seq . exon 10 90 . + . Parent=gene3 seq . exon 110 190 . + . Parent=gene3 seq . exon 201 290 . + . Parent=gene3 ### seq . gene 181 290 . + . ID=gene4 seq . exon 181 190 . + . Parent=gene4 seq . exon 201 290 . + . Parent=gene4 ###
To compute the consensus spliced alignments we call:
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$ gt csa csa_example_spliced_alignments.gff3
Which returns:
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##gff-version 3 ##sequence-region seq 1 290 seq gt csa gene 1 290 . + . ID=gene1 seq gt csa mRNA 1 290 . + . ID=mRNA1;Parent=gene1 seq gt csa exon 1 90 . + . Parent=mRNA1 seq gt csa exon 110 190 . + . Parent=mRNA1 seq gt csa exon 201 290 . + . Parent=mRNA1 seq gt csa mRNA 1 290 . + . ID=mRNA2;Parent=gene1 seq gt csa exon 1 90 . + . Parent=mRNA2 seq gt csa exon 101 190 . + . Parent=mRNA2 seq gt csa exon 201 290 . + . Parent=mRNA2 ###
As one can see, they have been combined into a consensus spliced alignment (represented as genes with mRNAs as children which in turn have exons as children) with two alternative splice forms. The first and the third spliced alignment have been combined into the first alternative splice form (mRNA1) and the the second and the fourth spliced alignment into the second alternative splice form (mRNA2).
As one can see, the second exon from the first alternative splice form is shorter than the corresponding exon from the second alternative splice form.