From a5c2d05d6febad2babe8d3f775f798bd5e5aa0c0 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 10 Mar 2019 16:59:28 -0500
Subject: [PATCH] Update README.md
---
README.md | 55 ++++++++++++++++++++++++++++++++++++++++++++++++++-----
1 file changed, 50 insertions(+), 5 deletions(-)
diff --git a/README.md b/README.md
index 708a93a..56f8013 100755
--- a/README.md
+++ b/README.md
@@ -19,26 +19,71 @@ To Run:
* **--fastq**
* path to the fastq location
* R1 and R2 only necessary but can include I2
- * eg: **--fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v2s2r100k/\*.fastq.gz'**
+ * eg: **--fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v3s2r100k/\*.fastq.gz'**
* **--designFile**
* path to design file (csv format) location
* column 1 = "Sample"
* column 2 = "fastq_R1"
* column 3 = "fastq_R2"
* can have repeated "Sample" if there are multiole fastq R1/R2 pairs for the samples
- * eg: **--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v2s2r100k/design.csv'**
+ * eg: **--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v3s2r100k/design.csv'**
* **--genome**
+ * reference genome
+ * requires workflow/conf/biohpc.config to work
* name of available 10x Gemomics premade reference genomes:
* *'GRCh38-3.0.0'* = Human GRCh38 release 93
- * *'GRCh38-3.0.0'* = Human GRCh38 release 93
- * *'GRCh38-3.0.0'* = Human GRCh38 release 93
- * *'GRCh38-3.0.0'* = Human GRCh38 release 93
+ * *'GRCh38-1.2.0'* = Human GRCh38 release 84
+ * *'hg19-3.0.0'* = Human GRCh37 (hg19) release 87
+ * *'hg19-1.2.0'* = Human GRCh37 (hg19) release 84
+ * *'mm10-3.0.0'* = Human GRCm38 (mm10) release 93
+ * *'mm10-3.0.0'* = Human GRCm38 (mm10) release 84
+ * *'hg19_and_mm10-3.0.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 93
+ * *'hg19_and_mm10-1.2.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84
+ * *'ercc92-1.2.0'* = ERCC.92 Spike-In
+ * if --genome is used then --genomeLocationFull is not necessary
+ * eg: **--genome 'GRCh38-3.0.0'**
* **--genomeLocationFull**
+ * path to a custom genome
+ * if --genomeLocationFull is used --genome is not necessary and is overwritten
+ * eg. **--genomeLocationFull '/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0'**
* **--expectCells**
+ * expected number of cells to be detected
+ * guides cellranger in it's cutoff for background/low quality cells
+ * as a guide it doesn't have to be exact
+ * 0-10000
+ * if --expextedCells is used then --forceCells is not necessary
+ * only used if --forceCells is not entered or set to 0
+ * eg: **--expectCells 10000**
* **--forceCells**
+ * forces filtering of the top number of cells matching this parameter
+ * 0-10000
+ * if --forceCells is used then --expectedCells is not necessary and is overwritten
+ * eg: **--forceCells 10000**
* **--kitVersion**
+ * the library chemistry version number for the 10x Genomics Gene Expression kit
+ * setting to auto will attempt to autodetect from the detected cycle strategy in the fastq's
+ * version numbers are spelled out
+ * --kitversion is only used if --version (cellranger version) is > 2
+ * --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
+ * options:
+ * *'auto'*
+ * *'three'*
+ * *'two'*
+ * eg: **--kitVersion 'three'**'
* **--version**
+ * cellranger version
+ * --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
+ * options:
+ * *'3.0.2'*
+ * *'3.0.1'*
+ * *'2.1.1'*
+ * eg: **--version '3.0.2'**'
* **--outDir**
+ * optional output directory for run
+ * eg: **--outDir 'test'**
+ * FULL EXAMPLE:
+
+**nextflow main.nf --fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v3s2r100k/\*.fastq.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v3s2r100k/design.csv' --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2' --outDir 'test'**
* Design example:
--
GitLab