curve2hints1
Tool to make exon segmentation and grouping the exons together to form augustus hints
Usage
curve2hints --in=file
--outexons=out.gff
--c=int
--s=float
Options
-
--in=s -
iput file is single file containing tracks in wig format
-
--outexons=s -
file for the output segmentaion
-
--c -
specify the threshold to distinguish between introns and exons in terms of coverage depths (default 4)
-
--s -
specify the ratio
(1-lambda1)/(1-lambda2)It should be >1 (default 1.12)
-
--z -
specify the chunk size (default value 50000)
-
--r -
To enable re-estimation of distribution from the output produced
-
--train_file -
Specify the gff file to be used for training the distributions.It should contain the position of both introns and exons
-
--bed_file -
Specify the output bedfile which contains the position of gene jumps (default: output.bed)
-
--augustus_hints -
Specify the output augustus hint file(default: augustus_hints.gff)
Additional documentation
An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.