NAME

digitagCT - Post-processing tool for DGE tags mapped using CRAC software.

SYNOPSIS

  digitagCT --gff file.gff dge.sam [--sage sage.csv] [--rna-seq rna-seq.sam] [--tar tar.bed(.gz)]

  dge.sam: a file with mapping information for each tag in SAM standard format. 

DESCRIPTION

AUTHOR

Nicolas PHILIPPE <nicolas.philippe@inserm.fr>, Alban MANCHERON <alban.mancheron@lirmm.fr> AND Jerome AUDOUX <jerome.audoux@univ-montp2.fr>

OPTIONS

  --gff=file.gff                  Specify GFF3 file to perform annotation with. (or declare ANNOTATION_GFF in conf file) 
  --est=file.gff                  Specify GFF3 file with EST annotations. These annotations will be used if we don't find any matching annotation in the --gff annotation file.
  --sage=sage.csv                 Specify a csv file exported by TranscriRef database with all sage/DGE tag features.
  --rna-seq= [1.sam, ..., N.sam]  Specify a list of sam file generated by CRAC software from RNA-Seq reads.
  --tar=tar.bed                   Specify a bed file exported by UCSC Genome Browser with all tiling arrays features. This file can be gzipped.
  --tag-occ                       Specify a tsv file with occurences for each tag (Tag_sequence\tNb_occ)
  --stranded                      This option is used to specify if rna-seq data are stranded.
  --summary=summary.txt           Specify a file to print the annotation summary.
  --conf=CracTools.cfg            Specify a specific configuration file.
  --help                          Print this message.
  --man                           Open man page.