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Consistent naming for summarizedexperiment outputs
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‎docs/output.md‎

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@@ -215,6 +215,21 @@ When `--remove_ribo_rna` is specified, the pipeline uses [SortMeRNA](https://git
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- `star_salmon/`
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- `*.Aligned.out.bam`: If `--save_align_intermeds` is specified the original BAM file containing read alignments to the reference genome will be placed in this directory.
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- `*.Aligned.toTranscriptome.out.bam`: If `--save_align_intermeds` is specified the original BAM file containing read alignments to the transcriptome will be placed in this directory.
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- `salmon.merged.gene_counts.tsv`: Matrix of gene-level raw counts across all samples.
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- `salmon.merged.gene_tpm.tsv`: Matrix of gene-level TPM values across all samples.
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- `salmon.merged.gene.SummarizedExperiment.rds`: RDS object that can be loaded in R that contains a [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) container with the abundance TPM (`tpm`), estimated counts (`counts`) and gene length (`length`), estimated library size-scaled counts (`counts_scaled`), estimated length-scaled counts (`counts_length_scaled`) in the assays slot for genes.
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- `salmon.merged.gene_lengths.tsv`: Matrix of average within-sample transcript lengths for each gene across all samples.
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- `salmon.merged.gene_counts_scaled.tsv`: Matrix of gene-level library size-scaled estimated counts across all samples.
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- `salmon.merged.gene_counts_length_scaled.tsv`: Matrix of gene-level length-scaled estimated counts across all samples.
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- `salmon.merged.transcript_counts.tsv`: Matrix of isoform-level raw counts across all samples.
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- `salmon.merged.transcript_tpm.tsv`: Matrix of isoform-level TPM values across all samples.
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- `tx2gene.tsv`: Tab-delimited file containing gene to transcripts ids mappings.
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- `salmon.merged.transcript.SummarizedExperiment.rds`: RDS object that can be loaded in R that contains a [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) container with the abundance TPM (`tpm`), estimated isoform-level raw counts (`counts`) and transcript length (`length`) in the assays slot for transcripts.
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- `star_salmon/<SAMPLE>/`
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- `quant.sf`: Salmon transcript-level quantification results.
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- `quant.genes.sf`: Salmon gene-level quantification results.
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- `star_salmon/<SAMPLE>/logs/`
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- `salmon_quant.log`: Salmon quantification log file.
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- `star_salmon/log/`
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- `*.SJ.out.tab`: File containing filtered splice junctions detected after mapping the reads.
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- `*.Log.final.out`: STAR alignment report containing the mapping results summary.
@@ -224,6 +239,23 @@ When `--remove_ribo_rna` is specified, the pipeline uses [SortMeRNA](https://git
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</details>
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:::tip
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You can access specific assay matrices from the `SummarizedExperiment` RDS object with the following R code:
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:::
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```r
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library(SummarizedExperiment)
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# Load the RDS object
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se <- readRDS("salmon.merged.gene.SummarizedExperiment.rds")
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# View available assays
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assayNames(se)
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# Access a specific assay, e.g., length-scaled counts
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assay(se, "counts_length_scaled")
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```
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[STAR](https://github.com/alexdobin/STAR) is a read aligner designed for splice aware mapping typical of RNA sequencing data. STAR stands for *S*pliced *T*ranscripts *A*lignment to a *R*eference, and has been shown to have high accuracy and outperforms other aligners by more than a factor of 50 in mapping speed, but it is memory intensive. Using `--aligner star_salmon` is the default alignment and quantification option.
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The STAR section of the MultiQC report shows a bar plot with alignment rates: good samples should have most reads as _Uniquely mapped_ and few _Unmapped_ reads.
@@ -728,14 +760,14 @@ The principal output files are the same between Salmon and Kallisto:
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- `<pseudo_aligner>/`
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- `<pseudo_aligner>.merged.gene_counts.tsv`: Matrix of gene-level raw counts across all samples.
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- `<pseudo_aligner>.gene_tpm.tsv`: Matrix of gene-level TPM values across all samples.
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- `all_samples_gene.SummarizedExperiment.rds`: RDS object that can be loaded in R that contains a [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) container with the abundance TPM (`tpm`), estimated counts (`counts`) and gene length (`length`), estimated library size-scaled counts (`counts_scaled`), estimated length-scaled counts (`counts_length_scaled`) in the assays slot for genes.
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- `<pseudo_aligner>.merged.gene.SummarizedExperiment.rds`: RDS object that can be loaded in R that contains a [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) container with the abundance TPM (`tpm`), estimated counts (`counts`) and gene length (`length`), estimated library size-scaled counts (`counts_scaled`), estimated length-scaled counts (`counts_length_scaled`) in the assays slot for genes.
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- `<pseudo_aligner>.merged.gene_lengths.tsv`: Matrix of average within-sample transcript lengths for each gene across all samples.
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- `<pseudo_aligner>.merged.gene_counts_scaled.tsv`: Matrix of gene-level library size-scaled estimated counts across all samples.
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- `<pseudo_aligner>.merged.gene_counts_length_scaled.tsv`: Matrix of gene-level length-scaled estimated counts across all samples.
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- `<pseudo_aligner>.merged.transcript_counts.tsv`: Matrix of isoform-level raw counts across all samples.
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- `<pseudo_aligner>.merged.transcript_tpm.tsv`: Matrix of isoform-level TPM values across all samples.
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- `tx2gene.tsv`: Tab-delimited file containing gene to transcripts ids mappings.
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- `all_samples_transcript.SummarizedExperiment.rds`: RDS object that can be loaded in R that contains a [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) container with the abundance TPM (`tpm`), estimated isoform-level raw counts (`counts`) and transcript length (`length`) in the assays slot for transcripts.
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- `<pseudo_aligner>.merged.transcript.SummarizedExperiment.rds`: RDS object that can be loaded in R that contains a [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) container with the abundance TPM (`tpm`), estimated isoform-level raw counts (`counts`) and transcript length (`length`) in the assays slot for transcripts.
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:::tip
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You can access specific assay matrices from the `SummarizedExperiment` RDS object with the following R code:
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library(SummarizedExperiment)
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# Load the RDS object
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se <- readRDS("all_samples_gene.SummarizedExperiment.rds")
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se <- readRDS("salmon.merged.gene.SummarizedExperiment.rds") # or kallisto.merged.gene.SummarizedExperiment.rds
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# View available assays
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assayNames(se)

‎tests/default.nf.test.snap‎

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‎tests/featurecounts_group_type.nf.test.snap‎

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‎tests/hisat2.nf.test.snap‎

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‎tests/kallisto.nf.test.snap‎

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‎tests/min_mapped_reads.nf.test.snap‎

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‎tests/nofasta.nf.test.snap‎

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‎tests/remove_ribo_rna.nf.test.snap‎

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‎tests/salmon.nf.test.snap‎

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‎tests/sentieon_default.nf.test.snap‎

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