Adding recommended parameters for 3' tag RNA-seq (e.g. QuantSeq) data

docs/usage.md

@@ -84,6 +84,37 @@ The `--umitools_grouping_method` parameter affects [how similar, but non-identic
 | In read name | [Illumina BCL convert >3.7.5](https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl_convert/bcl-convert-v3-7-5-software-guide-1000000163594-00.pdf)                                     | `--with_umi --skip_umi_extract --umitools_umi_separator ":"`                                                  |
 | In sequence  | [Takara Bio SMARTer® Stranded Total RNA-Seq Kit v3](https://www.takarabio.com/documents/User%20Manual/SMARTer%20Stranded%20Total%20RNA/SMARTer%20Stranded%20Total%20RNA-Seq%20Kit%20v3%20-%20Pico%20Input%20Mammalian%20User%20Manual-a_114949.pdf) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*"` |
 
+### 3′ digital gene expression assays
+
+Some bulk RNA-seq library preparation protocols capture only a 3' tag from each transcript, e.g. [3'Pool-seq](https://pubmed.ncbi.nlm.nih.gov/31959126/), [DRUG-seq](https://pubs.acs.org/doi/10.1021/acschembio.1c00920), [BRB-seq](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1671-x) or Lexogen's commercial [QuantSeq 3' mRNA-seq FWD](https://www.lexogen.com/quantseq-3mrna-sequencing/) protocol. The following parameters have been validated for `QuantSeq 3' mRNA-seq FWD` data, and provide useful starting points for other 3' RNA-seq protocols:
+
+#### Custom STAR parameters
+
+Lexogen provides an example analysis workflow [on their website](https://www.lexogen.com/quantseq-data-analysis/), which includes the _ENCODE standard options_ for the [STAR aligner]([https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf](https://github.com/alexdobin/STAR)). In addition, Lexogen also decreases the tolerance for mismatches and clips poly(A) tails. To apply these settings, add the following parameters to your `nextflow run` command (or provide them in a config file):
+
+```
+--extra_star_align_args "--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMultimapNmax 20 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA"
+```
+
+#### Custom Salmon arguments
+
+[Salmon's default quantitation algorithm](https://www.nature.com/articles/nmeth.4197) takes into account transcript length.
+Because 3' tag protocols do not capture full transcripts, this feature needs to be deactivated by specifying:
+
+```
+--extra_salmon_quant_args "--noLengthCorrection"
+```
+
+#### QuantSeq UMI module
+
+If unique molecular identifiers were used to prepare the library, add the following arguments as well, to extract the UMIs and deduplicated alignments:
+
+```
+--with_umi
+--umitools_extract_method regex
+--umitools_bc_pattern "^(?P<umi_1>.{6})(?P<discard_1>.{4}).*"
+```
+
 ## Reference genome files
 
 Please refer to the [nf-core website](https://nf-co.re/usage/reference_genomes) for general usage docs and guidelines regarding reference genomes.