Provided by: genometools_1.5.1-2ubuntu1_amd64 
NAME
gt-csa - Transform spliced alignments from GFF3 file into consensus spliced alignments.
SYNOPSIS
gt csa [option ...] [GFF3_file]
OPTIONS
-join-length
set join length for the spliced alignment clustering (default: 300)
-v
be verbose (default: no)
-o
redirect output to specified file (default: undefined)
-gzip
write gzip compressed output file (default: no)
-bzip2
write bzip2 compressed output file (default: no)
-force
force writing to output file (default: no)
-help
display help and exit
-version
display version information and exit
DESCRIPTION
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):
##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:
$ gt csa csa_example_spliced_alignments.gff3
Which returns:
##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 ist shorter than the corresponding
exon from the second alternative splice form.
AUTHOR
Report bugs to <gt-users@genometools.org>.
10/10/2012 GT-CSA(1)