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
authors
Github user fmalmeida Github user maxulysse Github user Khajidu Github user apeltzer Github user pinin4fjords
get in touch
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Tools

simpleaf
BSD-3-Clause

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

github.com/COMBINE-lab/simpleaf