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MasonSplicing

Generic Workflow Nodes for KNIME: SeqAn version 2.3.2.201707261654 by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

Create transcripts from IN.fa using the annotations from IN.gff. The resulting transcripts are written to OUT.fa.

You can pass an optional VCF file IN.vcf and the transcripts will be created from the haplotypes stored in the VCF file.

Web Documentation for MasonSplicing

Options

version-check
Turn this option off to disable version update notifications of the application.
quiet
Low verbosity.
verbose
Higher verbosity.
very-verbose
Highest verbosity.
seed
Seed for random number generation.
haplotype-name-sep
String separating contig name from haplotype number.

Input Ports

Path to input GFF or GTF file, must be sorted by reference name. [gff,gtf]
Splicing will filter to the records that have this type. [,opt.]
Assign features to their parent using the tag with this name. [,opt.]
Path to FASTA file to read the reference from. [fa,fasta]
Path to the VCF file with variants to apply. [vcf,opt.]

Output Ports

Output of materialized contigs. [fa,fasta]

Views

MasonSplicing Std Output
The text sent to standard out during the execution of MasonSplicing.
MasonSplicing Error Output
The text sent to standard error during the execution of MasonSplicing. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Update Site

To use this node in KNIME, install Generic Workflow Nodes for KNIME: SeqAn from the following update site:

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