Description

Import transcript-level abundances and estimated counts for gene-level analysis packages

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

quants/*{:bash}

:file

Quantification files

meta2{:bash}

:map

Groovy Map containing reference information related to the species reference e.g. [ id:'yeast' ]

tx2gene{:bash}

:file

A transcript to gene mapping table such as those generated by custom/tx2gene

*.{csv,tsv}

quant_type{:bash}

:string

Quantification type, kallisto, salmon, or rsem

Output

name:type
description
pattern

tpm_gene{:bash}

meta{:bash}

:map

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

*gene_tpm.tsv{:bash}

:file

Abundance (TPM) values derived from tximport output after summarizeToGene(), without a ‘countsFromAbundance’ specification

*gene_tpm.tsv

counts_gene{:bash}

meta{:bash}

:map

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

*gene_counts.tsv{:bash}

:file

Count values derived from tximport output after summarizeToGene(), without a ‘countsFromAbundance’ specification

*gene_counts.tsv

counts_gene_length_scaled{:bash}

meta{:bash}

:map

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

*gene_counts_length_scaled.tsv{:bash}

:file

Count values derived from tximport output after summarizeToGene(), with a ‘countsFromAbundance’ specification of ‘lengthScaledTPM’

*gene_counts_length_scaled.tsv

counts_gene_scaled{:bash}

meta{:bash}

:map

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

*gene_counts_scaled.tsv{:bash}

:file

Count values derived from tximport output after summarizeToGene(), with a ‘countsFromAbundance’ specification of ‘scaledTPM’

*gene_counts_scaled.tsv

lengths_gene{:bash}

meta{:bash}

:map

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

*gene_lengths.tsv{:bash}

:file

Length values derived from tximport output after summarizeToGene(), without a ‘countsFromAbundance’ specification

*gene_lengths.tsv

tpm_transcript{:bash}

meta{:bash}

:map

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

*transcript_tpm.tsv{:bash}

:file

Abundance (TPM) values derived from tximport output without summarizeToGene(), without a ‘countsFromAbundance’ specification

*transcript_tpm.tsv

counts_transcript{:bash}

meta{:bash}

:map

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

*transcript_counts.tsv{:bash}

:file

Count values derived from tximport output without summarizeToGene(), without a ‘countsFromAbundance’ specification

*transcript_counts.tsv

lengths_transcript{:bash}

meta{:bash}

:map

Groovy Map containing information related to the experiment as a whole e.g. [ id:'SRP123456' ]

*transcript_lengths.tsv{:bash}

:file

Length values derived from tximport output without summarizeToGene(), without a ‘countsFromAbundance’ specification

*gene_lengths.tsv

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
circrnariboseqrnaseq
maintainer
Github user pinin4fjords
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