modules/tximeta_tximport
Import transcript-level abundances and estimated counts for gene-level analysis packages
Description
Import transcript-level abundances and estimated counts for gene-level analysis packages
Input
Groovy Map containing information related to the experiment as a whole
e.g. [ id:'SRP123456' ]
Groovy Map containing reference information related to the species
reference e.g. [ id:'yeast' ]
A transcript to gene mapping table such as those generated by custom/tx2gene
*.{csv,tsv} Groovy Map containing information related to the experiment as a whole
e.g. [ id:'SRP123456' ]
Optional ‘coldata’ file equivalent to a sample sheet where the first
column corresponds to the sample names (directory names in the input
salmon/ kallisto results)
*.{csv,tsv} Output
Groovy Map containing information related to the experiment as a whole
e.g. [ id:'SRP123456' ]
Abundance (TPM) values derived from tximport output after
summarizeToGene(), without a ‘countsFromAbundance’ specification
*gene_tpm.tsv Count values derived from tximport output after
summarizeToGene(), without a ‘countsFromAbundance’ specification
*gene_counts.tsv Count values derived from tximport output after summarizeToGene(), with
a ‘countsFromAbundance’ specification of ‘lengthScaledTPM’
*gene_counts_length_scaled.tsv Count values derived from tximport output after summarizeToGene(), with
a ‘countsFromAbundance’ specification of ‘scaledTPM’
*gene_counts_scaled.tsv Length values derived from tximport output after summarizeToGene(),
without a ‘countsFromAbundance’ specification
*gene_lengths.tsv Abundance (TPM) values derived from tximport output without
summarizeToGene(), without a ‘countsFromAbundance’ specification
*transcript_tpm.tsv Count values derived from tximport output without
summarizeToGene(), without a ‘countsFromAbundance’ specification
*transcript_counts.tsv Length values derived from tximport output without summarizeToGene(),
without a ‘countsFromAbundance’ specification
*gene_lengths.tsv 