Up: Component summary Component

AligFilterMatches

Allows filtering of alignments in BAM/SAM files, mainly output from Tophat

Version 1.0
Bundle sequencing
Categories
Authors Alejandra Cervera (alejandra.cervera@helsinki.fi)
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Requires samtools ; installer (bash)
Source files component.xml aligFilter.sh
Usage Example with default values

Inputs

Name Type Mandatory Description
accepted_hits BAM Mandatory The aligned RNA-seq reads in BAM format.

Outputs

Name Type Description
dataOut1 SAM A SAM file filtered.
dataOut2 SAM A SAM file filtered.

Parameters

Name Type Default Description
cutoff int 1 The maximum number of alignments for each read wanted in the output.

Test cases

Test case Parameters IN
accepted_hits
OUT
dataOut1
OUT
dataOut2
case1 properties accepted_hits (missing) (missing)

# Testing AligFilterMatches component,
cutoff = 1


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