clarification of star and salmon outputs from issue #722

Author: ctuni

docs/output.md

@@ -657,13 +657,13 @@ Results generated by MultiQC collate pipeline QC from supported tools i.e. FastQ
   - `salmon.merged.gene_counts.tsv`: Matrix of gene-level raw counts across all samples.
   - `salmon.merged.gene_tpm.tsv`: Matrix of gene-level TPM values across all samples.
   - `salmon.merged.gene_counts.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 TPM (`abundance`), estimated counts (`counts`) and transcript length (`length`) in the assays slot for genes.
-  - `salmon.merged.gene_counts_scaled.tsv`: Matrix of gene-level scaled counts across all samples.
-  - `salmon.merged.gene_counts_scaled.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 TPM (`abundance`), estimated counts (`counts`) and transcript length (`length`) in the assays slot for genes.
+  - `salmon.merged.gene_counts_scaled.tsv`: Matrix of gene-level library size-scaled counts across all samples.
+  - `salmon.merged.gene_counts_scaled.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 TPM (`abundance`), estimated library size-scaled counts (`counts`) and transcript length (`length`) in the assays slot for genes.
   - `salmon.merged.gene_counts_length_scaled.tsv`: Matrix of gene-level length-scaled counts across all samples.
-  - `salmon.merged.gene_counts_length_scaled.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 TPM (`abundance`), estimated counts (`counts`) and transcript length (`length`) in the assays slot for genes.
+  - `salmon.merged.gene_counts_length_scaled.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 TPM (`abundance`), estimated length-scaled counts (`counts`) and transcript length (`length`) in the assays slot for genes.
   - `salmon.merged.transcript_counts.tsv`: Matrix of isoform-level raw counts across all samples.
   - `salmon.merged.transcript_tpm.tsv`: Matrix of isoform-level TPM values across all samples.
-  - `salmon.merged.transcript_counts.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 TPM (`abundance`), estimated counts (`counts`) and transcript length (`length`) in the assays slot for transcripts.
+  - `salmon.merged.transcript_counts.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 TPM (`abundance`), estimated isoform-level raw counts (`counts`) and transcript length (`length`) in the assays slot for transcripts.
   - `salmon_tx2gene.tsv`: Tab-delimited file containing gene to transcripts ids mappings.
 - `salmon/<SAMPLE>/`
   - `aux_info/`: Auxiliary info e.g. versions and number of mapped reads.
@@ -676,7 +676,7 @@ Results generated by MultiQC collate pipeline QC from supported tools i.e. FastQ
 
 </details>
 
-As described in the [STAR and Salmon](#star-and-salmon) section, you can choose to pseudo-align and quantify your data with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html) by providing the `--pseudo_aligner salmon` parameter. By default, Salmon is run in addition to the standard alignment workflow defined by `--aligner`, mainly because it allows you to obtain QC metrics with respect to the genomic alignments. However, you can provide the `--skip_alignment` parameter if you would like to run Salmon in isolation.
+As described in the [STAR and Salmon](#star-and-salmon) section, you can choose to pseudo-align and quantify your data with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html) by providing the `--pseudo_aligner salmon` parameter. By default, Salmon is run in addition to the standard alignment workflow defined by `--aligner`, mainly because it allows you to obtain QC metrics with respect to the genomic alignments. However, you can provide the `--skip_alignment` parameter if you would like to run Salmon in isolation. If Salmon is run in isolation, the outputs mentioned above will be found in a folder named `salmon`. If Salmon is run alongside STAR, the folder will be named `star_salmon`.
 
 Transcripts with large inferential uncertainty won't be assigned the exact number of reads reproducibly, every time Salmon is run. Read more about this on the [nf-core/rnaseq](https://github.com/nf-core/rnaseq/issues/585) and [salmon](https://github.com/COMBINE-lab/salmon/issues/613) Github repos.