MasonSplicing

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

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Path to input GFF or GTF file, must be sorted by reference name. [gff,gff.bgzf,gff.gz,gff3,gff3.bgzf,gff3.gz,gtf,gtf.bgzf,gtf.gz]
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Splicing will filter to the records that have this type. [,opt.]
Icon
Assign features to their parent using the tag with this name. [,opt.]
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Path to FASTA file to read the reference from. [fq,fq.bgzf,fq.gz,fastq,fastq.bgzf,fastq.gz,fa,fa.bgzf,fa.gz,fasta,fasta.bgzf,fasta.gz,faa,faa.bgzf,faa.gz,ffn,ffn.bgzf,ffn.gz,fna,fna.bgzf,fna.gz,frn,frn.bgzf,frn.gz,embl,embl.bgzf,embl.gz,gbk,gbk.bgzf,gbk.gz,raw,raw.bgzf,raw.gz,sam,sam.bgzf,sam.gz,bam]
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Path to the VCF file with variants to apply. [vcf,vcf.bgzf,vcf.gz,opt.]

Output Ports

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Output of materialized contigs. [fq,fq.bgzf,fq.gz,fastq,fastq.bgzf,fastq.gz,fa,fa.bgzf,fa.gz,fasta,fasta.bgzf,fasta.gz,faa,faa.bgzf,faa.gz,ffn,ffn.bgzf,ffn.gz,fna,fna.bgzf,fna.gz,frn,frn.bgzf,frn.gz,raw,raw.bgzf,raw.gz,sam,sam.bgzf,sam.gz,bam]

Popular Predecessors

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Popular Successors

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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.)

Workflows

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Further Links

Developers

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