Description

Indexing of transcriptome for gene expression quantification using SimpleAF

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing information on genome_fasta

genome_fasta (file)

FASTA file containing the genome sequence

meta2 (map)

Groovy Map containing information on genome_gtf

genome_gtf (file)

GTF file containing transcript annotations. Optional if transcript FASTA file is provided.

meta3 (map)

Groovy Map containing information on transcript_fasta

transcript_fasta (file)

FASTA file containing the transcript sequences. Optional if transcript GTF file is provided.

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing information on genome_fasta or transcript_fasta (whichever was used)

index (directory)

Folder containing the Salmon index files

salmon/index

transcript_tsv (file)

Transcript-to-gene mapping file in 3-column TSV format

salmon/ref/*_t2g_3col.tsv

salmon (directory)

Folder containing the Salmon files

salmon

versions (file)

File containing software versions

versions.yml

Tools

simpleaf
BSD-3-Clause

SimpleAF is a tool for quantification of gene expression from RNA-seq data