NAME
curve2hints - tool to make exon segmentation and grouping the exons together to form AUGUSTUS hints
SYNOPSIS
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)
AUTHORS
AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
ADDITIONAL DOCUMENTATION
An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.