File: curve2hints.1.adoc

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# 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. K├Ânig, L. Gerischer and L. Romoth.

## ADDITIONAL DOCUMENTATION

An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.