update readme

umccr · Jun 19, 2024 · e0399c8 · e0399c8
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diff --git a/README.Rmd b/README.Rmd
@@ -63,8 +63,7 @@ below. For more details, see [workflow.md](/workflow.md).
 
 <img src="man/figures/RNAsum_workflow.png" width="100%">
 
-1. Collect patient **WTS data** from the [DRAGEN RNA][dragen-rna]
-   pipeline including per-gene read counts and gene fusions.
+1. Collect sample **WTS data** including per-gene read counts and gene fusions.
 2. Add expression data from **[reference cohorts](#reference-data)** to get an
    idea about the expression levels of genes of interest in other cancer patient
    cohorts. The read counts are normalised, transformed and converted into a scale
@@ -83,14 +82,12 @@ below. For more details, see [workflow.md](/workflow.md).
    plots presenting expression levels of the genes of interest. The report
    consists of several sections described [here](./articles/report_structure.md).
 
-[dragen-rna]: <https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/edico-genome-inc-dragen-rna-pipeline.html>
-
 ## Reference data
 
 The reference expression data are available for **33 cancer types** and were
 derived from [external](#external-reference-cohorts)
 ([TCGA](https://tcga-data.nci.nih.gov/)) and [internal](#internal-reference-cohort)
-([UMCCR](https://research.unimelb.edu.au/centre-for-cancer-research/our-research/precision-oncology-research-group))
+([UMCCR](https://mdhs.unimelb.edu.au/centre-for-cancer-research/our-research/precision-oncology-research-group))
 resources.
 
 ### External reference cohorts
@@ -148,46 +145,45 @@ There are two rationales for using the internal reference cohort:
 
 ## Input data
 
-`RNAsum` accepts [WTS](#wts) data processed by the `DRAGEN RNA`
-pipeline. Additionally, the WTS data
-can be integrated with [WGS](#wgs)-based data processed using the
-`umccrise` pipeline. In the latter case, the genome-based findings from the
-corresponding patient sample are incorporated into the report and are used as a
+`RNAsum` accepts [WTS](#wts) data processed by the state-of-the-art bioinformatic
+tools such as kallisto and salmon for quantification and Arriba for fusion calling. 
+RNAsum can aso process and combine fusion output from Illumina's Dragen pipeline.
+Additionally, the WTS data can be integrated with [WGS](#wgs)-based data processed 
+using the tools discussed in the section [WGS](#wgs). 
+
+In the latter case, the genome-based findings from the
+corresponding sample are incorporated into the report and are used as a
 primary source for expression profile prioritisation.
 
 ### WTS
 
 The only required WTS input data are **read counts** provided in a
-quantification file from the `DRAGEN RNA` pipeline.
+quantification file.
 
-#### DRAGEN RNA
+#### RNA
 
 The table below lists all input data accepted in `RNAsum`:
 
 | Input file                             | Tool                                           | Example                                         | Required   |
 | -------------------------------------- | ---------------------------------------------- | ----------------------------------------------- | ---------- |
-| Quantified transcript **abundances**   | [salmon][salmon] ([description][salmon-res])   | [TEST.quant.sf][salmon-ex]                      | **Yes**    |
-| **Fusion gene** list                   | [DRAGEN RNA][dragen-rna]                       | [TEST.fusion_candidates.final][dragen-rna-ex]   | No         |
+| Quantified transcript **abundances**   | [salmon][salmon] ([description][salmon-res])   | [*.quant.sf][salmon-ex]                         | **Yes**    |
+| Quantified gene **abundances**         | [salmon][salmon] ([description][salmon-res])   | [*.quant.gene.sf][salmon-ex2]                   | **Yes**    |
+| **Fusion gene** list                   | [Arriba][arriba]                               | [fusions.tsv][dragen-rna-ex]                    | No         |
+| **Fusion gene** list                   | [DRAGEN RNA][dragen-rna]                       | [*.fusion_candidates.final][dragen-rna-ex]      | No         |
 
 [salmon]: <https://salmon.readthedocs.io/en/latest/salmon.html>
 [salmon-ex]: </inst/rawdata/test_data/dragen/TEST.quant.sf>
+[salmon-ex2]: </inst/rawdata/test_data/dragen/TEST.quant.gene.sf>
 [salmon-res]: <https://salmon.readthedocs.io/en/latest/file_formats.html#fileformats>
+[arriba]: <https://arriba.readthedocs.io/en/latest/>
+[arriba-res]: </inst/rawdata/test_data/final/test_sample_WTS/arriba/fusions.tsv>
 [dragen-rna]: <https://sapac.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/edico-genome-inc-dragen-rna-pipeline.html>
 [dragen-rna-ex]: </inst/rawdata/test_data/dragen/test_sample_WTS.fusion_candidates.final>
 
-These files are expected to be organised in the following structure:
-
-```text
-|
-|____<SampleName>
-  |____<SampleName>quant.sf
-  |____<SampleName>.fusion_candidates.final
-```
 
 ### WGS
 
-`RNAsum` is designed to be compatible with WGS outputs generated from
-`umccrise`.
+`RNAsum` is designed to be compatible with WGS outputs.
 
 The table below lists all input data accepted in `RNAsum`:
 
@@ -204,20 +200,6 @@ The table below lists all input data accepted in `RNAsum`:
 [manta]: <https://github.com/Illumina/manta>
 [manta-ex]: </inst/rawdata/test_data/umccrised/test_sample_WGS/structural/sv-prioritize-manta.tsv>
 
-These files are expected to be organised in the following structure:
-
-```text
-|
-|____umccrised
-  |____<SampleName>
-    |____pcgr
-    | |____<SampleName>-somatic.pcgr.snvs_indels.tiers.tsv
-    |____purple
-    | |____<SampleName>.purple.gene.cnv
-    |____structural
-      |____<SampleName>-manta.tsv
-```
-
 ## Usage
 
 ```{bash echo=TRUE, eval=FALSE}
@@ -242,23 +224,24 @@ echo ""
 
 Human reference genome
 ***[GRCh38](https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.39)***
-(*Ensembl* based annotation version ***86***) is used for gene annotation by
+(*Ensembl* based annotation version ***105***) is used for gene annotation by
 default. GRCh37 is no longer supported.
 
 ### Examples
 
 Below are `RNAsum` CLI commands for generating HTML reports under different
 data availability scenarios:
 
-1. [WTS data only](#1-wts-data-only)
-2. [WTS and WGS data](#2-wts-and-wgs-data)
+
+1. [WTS and WGS data](#1-wts-and-wgs-data)
+2. [WTS data only](#2-wts-data-only)
 3. [WTS WGS and clinical data](#3-wts-wgs-and-clinical-data)
 
 **Note**
 
 * Example data is provided in the `/inst/rawdata/test_data` folder of the GitHub
   [repo][rnasum-gh].
-* The `RNAsum` runtime should be less than **20 minutes** using **16GB RAM**
+* The `RNAsum` runtime should be less than **15 minutes** using **16GB RAM**
   memory and **1 CPU**.
 
 #### 1. WTS and WGS data
@@ -267,9 +250,8 @@ This is the **most frequent and preferred case**, in which the
 [WGS](#wgs)-based findings will be used as a primary source for expression
 profile prioritisation. The genome-based results can be incorporated into the
 report by specifying the location of the corresponding
-`umccrise` output files (including results from `PCGR`, `PURPLE`, and `Manta`)
-using the `--umccrise` argument. The **`Mutated genes`**,
-**`Structural variants`** and **`CN altered genes`** report sections will
+output files (including results from `PCGR`, `PURPLE`, and `Manta`). 
+The **`Mutated genes`**, **`Structural variants`** and **`CN altered genes`** report sections will
 contain information about expression levels of the mutated genes,
 genes located within detected SVs and CN altered regions, respectively.
 The results in the **`Fusion genes`** section will be ordered based on the
@@ -280,9 +262,12 @@ adenocarcinoma dataset is used as reference cohort (`--dataset TEST `).
 rnasum.R \
   --sample_name test_sample_WTS \
   --dataset TEST \
-  --dragen_rnaseq inst/rawdata/test_data/dragen \
+  --manta_tsv \
+  --pcgr_tiers_tsv \
+  --purple_gene_tsv \
+  --salmon \
+  --arriba_tsv \
   --report_dir inst/rawdata/test_data/dragen/RNAsum \
-  --umccrise inst/rawdata/test_data/umccrised/test_sample_WGS \
   --save_tables FALSE
 ```
 
@@ -292,7 +277,7 @@ The HTML report `test_sample_WTS.RNAsum.html` will be created in the
 #### 2. WTS data only
 
 In this scenario, only [WTS](#wts) data will be used and only expression levels
-of key **[`UMCCR Cancer genes`](https://github.com/umccr/umccrise/blob/master/workflow.md#key-cancer-genes)**,
+of key **[`Cancer genes`](https://github.com/umccr/umccrise/blob/master/workflow.md#key-cancer-genes)**,
 **`Fusion genes`**, **`Immune markers`** and homologous recombination deficiency
 genes (**`HRD genes`**) will be reported. Moreover, gene fusions reported in
 the `Fusion genes` report section will not contain information about evidence
@@ -303,7 +288,8 @@ is used as the reference cohort (`--dataset TEST`).
 rnasum.R \
   --sample_name test_sample_WTS \
   --dataset TEST \
-  --dragen_rnaseq inst/rawdata/test_data/dragen \
+  --salmon inst/rawdata/test_data/dragen \
+  --arriba \
   --report_dir inst/rawdata/test_data/dragen/RNAsum \
   --save_tables FALSE
 ```
@@ -386,4 +372,4 @@ that are presented in the HTML report.
 
 #### Code of Conduct
 
-The code of conduct can be accessed [here](./CODE_OF_CONDUCT.md).
+The code of conduct can be accessed [here](./CODE_OF_CONDUCT.md)