Update docs/output.md

Author: pinin4fjords

docs/output.md

@@ -728,7 +728,7 @@ The [tximport](https://bioconductor.org/packages/release/bioc/html/tximport.html
 According to the [`txtimport` documentation](https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#Downstream_DGE_in_Bioconductor) you can do one of the following:
 
 - Use the original (bias-uncorrected) counts _with an offset_: import all the salmon `quant.sf` files with `tximport` and then use `DESeq2` with `dds <- DESeqDataSetFromTximport(txi, sampleTable, ~condition)` to automatically construct an object with gene-level offsets in-built, which can be used by DESeq2 to automatically account for effective gene length effects across conditions. It's also possible to use the `.gene_lengths.tsv` matrices output by this workflow to make your own object the same way- which is what [the nf-core differentialabundance workflow does](https://nf-co.re/differentialabundance/1.5.0/docs/usage#outputs-from-nf-corernaseq-and-other-tximport-processed-results). See the [DESeq2 module](https://github.com/nf-core/modules/blob/c8f7f481bf2ccd8f9c7f2d499d94e74d4b9e23ab/modules/nf-core/deseq2/differential/templates/deseq_de.R#L323) for the implementation details.
-- Use bias-corrected counts _without an offset_: load and use `salmon.merged.gene_counts_length_scaled.tsv` or `salmon.merged.gene_counts_scaled.tsv` directly as you would with a regular gene-level counts matrix. These files were created using the `tximport` argument `countsFromAbundance="scaledTPM"` or `"lengthScaledTPM"` to scale counts to library size or to library size and average transcript length respectively, forgoing the need for an offset matrix.
+- Use bias-corrected counts _without an offset_: load and use `salmon.merged.gene_counts_length_scaled.tsv` or `salmon.merged.gene_counts_scaled.tsv` directly as you would with a regular gene-level counts matrix. These files were created using the `tximport` argument `countsFromAbundance="scaledTPM"` or `"lengthScaledTPM"` to scale counts to library size or to library size and average transcript length respectively.
 - Use the original (bias-uncorrected) counts _without an offset_: load and use the `txi$counts` matrix (or `salmon.merged.gene_counts.tsv`) with `DESeq2`. This is generally **not** recommended, since it does not correct for potential differential isoform usage (the offset). However, if you have 3’ tagged RNA-seq data, then this _is_ the most suitable method, because the counts do not exhibit any length bias.
 
 > **NB:** The default Salmon parameters and a k-mer size of 31 are used to create the index. As [documented here](https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode) and [discussed here](https://github.com/COMBINE-lab/salmon/issues/482#issuecomment-583799668), a k-mer size off 31 works well with reads that are 75bp or longer.