subworkflows/quantify_pseudo_alignment
Perform quantification with Salmon or Kallisto to produce count tables and SummarizedExperiment objects
Description
Perform quantification with Salmon or Kallisto to produce count tables and SummarizedExperiment objects
Input
Sample sheet, to be baked into the colData
of summarizedexperiment
objects.
*.{csv,tsv}
Channel with input FastQ files of size 1 and 2 for single-end and
paired-end data, respectively. OR a transcriptome-level BAM file if
running Salmon in alignment mode.
Channel with features in GTF format. Passed to pseudoaligners and used
to generate transcript/ gene mappings.
Estimated fragment length. Required if running Kallisto with
single-ended reads.
Output
Channel containing those pseudoaligner outputs readable by MultiQC for
passing to workflow-level reporting.
Gene-level matrix of unadjusted estimated counts from tximport
(countsFromAbundance = 'no'
).
*.gene_counts.tsv
Gene-level matrix of length values for modelling in downstream
analysis.
gene_lengths.tsv
Gene-level matrix of estimated counts, generated from abundance (TPM)
values by scaling to library size, additionally scaled using the
average transcript length, averaged over samples and to library size,
using tximport countsFromAbundance = 'lengthScaledTPM'
.
*.gene_counts_length_scaled.tsv
Gene-level matrix of estimated counts, generated from abundance (TPM)
values by scaling to library size with tximport countsFromAbundance = 'scaledTPM'
.
*.gene_counts_length_scaled.tsv
Transcript-level matrix of unadjusted estimated counts from tximport
(countsFromAbundance = 'no'
).
*.transcript_counts.tsv
Transcript-level matrix of length values for modelling in downstream
analysis.
transcript_lengths.tsv
Serialised SummarizedExperiment object containing gene level TPM
abundance values and counts generated from tximport with
countsFromAbundance = 'no'
.
*.rds
Serialised SummarizedExperiment object containing gene level TPM
abundance values and counts generated from tximport with
countsFromAbundance='lengthScaledTPM'
.
*.rds
Serialised SummarizedExperiment object containing gene level TPM
abundance values and counts generated from tximport with
countsFromAbundance='scaledTPM'
.
*.rds
Serialised SummarizedExperiment object containing transcript level TPM
abundance values and counts generated from tximport with
countsFromAbundance = 'no'
.
*.rds