NAME

MEME_XML_motif_extractor.pl - Compute sequence coverage statistics of motifs from MEME standard XML output

SYNOPSIS

MEME_XML_motif_extractor.pl [-f FILE] [-d STRING] [-o STRING] [-t STRING] [-x String] [-a STRING] [-r STRING]

DESCRIPTION

This program computes simple statistics from MEME XML output. It returns a list of found motifs with the number of sequences containing those motifs and produces nice ggplot graphs.

OPTIONS

-f

MEME xml output file

-d

Path to working dir containing the xml file

-o

Path to Output directory

-t

Name of output files

-x

If annotation is found in the sequence name fields, items that should not be analyzed (e.g. annnotion like miscRNA, ncRNA, predicted_gene) can be defined here

-a

Defined the type of nucleic acid in MEME input, defaults to DNA, can be ignored if protein sequences were used

-r

Path to the R library

--help -h

Print short help

--man

Prints the manual page and exits

AUTHOR

Joerg Fallmann <joerg.fallmann@univie.ac.at>