Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
C
cellranger_count
Manage
Activity
Members
Labels
Plan
Issues
11
Issue boards
Milestones
Iterations
Wiki
Requirements
Code
Merge requests
0
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Locked files
Build
Pipelines
Jobs
Pipeline schedules
Test cases
Artifacts
Deploy
Releases
Container Registry
Operate
Environments
Monitor
Incidents
Service Desk
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Code review analytics
Issue analytics
Insights
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
BICF
Astrocyte
cellranger_count
Commits
603c8398
Commit
603c8398
authored
5 years ago
by
Gervaise Henry
Browse files
Options
Downloads
Patches
Plain Diff
Update README.md
parent
e8ee7609
Branches
Branches containing commit
Tags
Tags containing commit
1 merge request
!53
Develop
Pipeline
#4329
failed with stages
in 5 minutes and 17 seconds
Changes
1
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
README.md
+66
-66
66 additions, 66 deletions
README.md
with
66 additions
and
66 deletions
README.md
+
66
−
66
View file @
603c8398
...
...
@@ -24,73 +24,73 @@ To Run:
*
Available parameters:
*
**--fastq**
*
path to the fastq location
*
R1 and R2 only necessary but can include I2
*
only fastq's in designFile (see below) are used, not present will be ignored
*
eg:
**--fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/\*.fastq.gz'**
*
path to the fastq location
*
R1 and R2 only necessary but can include I2
*
only fastq's in designFile (see below) are used, not present will be ignored
*
eg:
**--fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.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 multiple fastq R1/R2 pairs for the samples
*
can be downloaded
[
HERE
](
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/master/docs/design.csv
)
*
eg:
**--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.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
*
*'GRCh38-1.2.0'*
= 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'*
= Mouse GRCm38 (mm10) release 93
*
*'mm10-3.0.0'*
= Mouse 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 ignored
*
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 ignored
*
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 sequencing 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:
*
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 multiple fastq R1/R2 pairs for the samples
*
can be downloaded
[
HERE
](
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/master/docs/design.csv
)
*
eg:
**--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.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
*
*'GRCh38-1.2.0'*
= 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'*
= Mouse GRCm38 (mm10) release 93
*
*'mm10-3.0.0'*
= Mouse 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 ignored
*
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 ignored
*
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 sequencing 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 run workflow/main.nf --fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/\*.fastq.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/design.csv' --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2' --outDir 'test'**
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment