Add pairs task

Add pairs task

Process a previously segmented data by joining or breaking connected graphs using paired end data information. 

Command: java -Xmx2000m jar scripture.jar -task addpairs <Mandatory parameters>

Mandatory Parameters

-in: A graph output from a regular transcript run (segmentation task).

-out: Path to a file for Scripture to write its output. The output of Scripture is a BED file format containing all identified transcripts, additionally scripture also outputs a full graph file containing all segments found in the data (significant or not) to a file named after the value specified by this parameter but with an extra .dot extension. The format of the graph file is DOT. This file is self contained and can be used to estimate expression or further processing (e.g. add paired data if non was used when this task was ran). See extract task for information on how to view information in this file.

-sizeFile: A 2-column tab separated file containing the chromosome name and size for the organism.

-pairedEnd: Paired end data. This file can be in either SAM, BAM format and should contain the full insert  (from the start of the first pair to the end of the second pair) as it maps to the genome.