Detect the genes containing too much UTR's exon according to a choosen threshold. If no UTR option (3, 5, 3 and 5, both) is given the threshold will be not used. option 3 and 5 together is different of "both". In the first case the gene is discarded if either the 3' or the 5' UTR contains more exon than the threshold given. In the second case, will be discarded only the genes where the addition of UTR's exon of both side is over the threshold given.
agat_sp_manage_UTRs.pl --ref infile --three --five -p --out outFile agat_sp_manage_UTRs.pl --help
--gff, --ref, --reffile or -f
Input GTF/GFF file.
-n, -t, --nb or --number
Threshold of exon's number of the UTR. Over or equal to this threshold, the UTR will be discarded. Default value is 5.
-3, --three or --tree_prime_utr
The threshold of the option <n> will be applied on the 3'UTR.
-5, --five or --five_prime_utr
The threshold of the option <n> will be applied on the 5'UTR.
-b, --both or --bs
The threshold of the option <n> will be applied on genes where the number of UTR exon (3' and 5' additioned) is over it.
--p or --plot
Allows to create an histogram in pdf of UTR sizes distribution.
--out, --output or -o
Output gff3 file where the gene incriminated will be write.
--help or -h
Display this helpful text.