quant_tximport_summarizedexperiment

Post-process transcript-level quantification results using tximport to produce count matrices and SummarizedExperiment objects

rnaseqquantificationtximportsummarizedexperimentsalmonkallistorsem

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/quant_tximport_summarizedexperiment

Description

Post-process transcript-level quantification results using tximport to produce count matrices and SummarizedExperiment objects

Input

name

description

pattern

`samplesheet`

Sample sheet, to be baked into the colData of SummarizedExperiment
objects.

Structure: [ val(meta), path(samplesheet) ]

*.{csv,tsv}

`quant_results`

Per-sample quantification results. For Salmon these are result
directories containing quant.sf, for Kallisto directories containing
abundance.tsv, and for RSEM the .isoforms.results files. All samples
must have been quantified against the same transcriptome, as only a
single sample is used for transcript-to-gene mapping discovery. If
support for mixed transcriptomes is needed in future, tx2gene would
need to run independently per sample.

Structure: [ val(meta), path(results) ]

`gtf`

Channel with features in GTF format, used to generate transcript/gene
mappings via tx2gene.

`gtf_id_attribute`

Attribute in GTF file corresponding to the gene identifier.

`gtf_extra_attribute`

GTF alternative gene attribute (e.g. gene_name)

`quant_type`

Quantification tool type. One of ‘salmon’, ‘kallisto’, or ‘rsem’.

`skip_merge`

Skip cross-sample merging. When true, runs tximport per-sample
instead of collecting all samples, and skips SummarizedExperiment
creation. Useful for very large cohorts.

Output

name

description

pattern

`tx2gene`

Transcript-to-gene mapping file generated from the GTF.

*.tx2gene.tsv

`tx2gene_augmented`

tx2gene mapping table actually used by tximport, equal to the input
tx2gene with self-mappings appended for any transcripts present in the
quantification output but missing from the input. Use this file (not
tx2gene) to reproduce the published gene-level outputs from the
per-sample quantification files.

*tx2gene_augmented.tsv

`tpm_gene`

Gene-level matrix of abundance values in TPM.

*.gene_tpm.tsv

`counts_gene`

Gene-level matrix of unadjusted estimated counts from tximport
(countsFromAbundance = 'no').

*.gene_counts.tsv

`lengths_gene`

Gene-level matrix of effective length values.

*.gene_lengths.tsv

`counts_gene_length_scaled`

Gene-level matrix of estimated counts, generated from abundance (TPM)
values by scaling to library size, additionally scaled using the
average transcript length, using tximport
countsFromAbundance = 'lengthScaledTPM'.

*.gene_counts_length_scaled.tsv

`counts_gene_scaled`

Gene-level matrix of estimated counts, generated from abundance (TPM)
values by scaling to library size with tximport
countsFromAbundance = 'scaledTPM'.

*.gene_counts_scaled.tsv

`tpm_transcript`

Transcript-level matrix of abundance values in TPM.

*.transcript_tpm.tsv

`counts_transcript`

Transcript-level matrix of unadjusted estimated counts from tximport
(countsFromAbundance = 'no').

*.transcript_counts.tsv

`lengths_transcript`

Transcript-level matrix of effective length values.

*.transcript_lengths.tsv

`merged_gene_rds`

Serialised SummarizedExperiment object containing gene-level assays
(counts, length-scaled counts, scaled counts, lengths, TPM).

*.rds

`merged_transcript_rds`

Serialised SummarizedExperiment object containing transcript-level
assays (counts, lengths, TPM).