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CURVE2HINTS(1)   CURVE2HINTS(1)

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.