Commit 4140a140 authored by yy1533's avatar yy1533
Browse files

:book::feet: update quick-start based on new cmd calling and update Result section

parent 98d34209
......@@ -53,7 +53,22 @@ to 2 FASTQ files.
By running the pipeline of `celseq2` with the them, the users would get
UMI count matrix for each of the two plates.
## Step-1: Define Experiment Table
## Step-1: Specify Configuration of Workflow
Run `new-configuration-file` command to initiate configuration file (YAML
format), which specifies the details of CEL-Seq2 techniques the users perform,
and genome annotation information, etc.
This configuration can be shared and used more than once as long as user is
running pipeline on same specie.
``` bash
new-configuration-file -o /path/to/wonderful_CEL-Seq2_config.yaml
```
Example of configuration is [here](https://gitlab.com/Puriney/celseq2/blob/master/example/config.yaml).
## Step-2: Define Experiment Table
Run `new-experiment-table` command to initiate table file (space/tab separated
file) to specify the experiment layout.
......@@ -85,19 +100,6 @@ indexed from 1 to 8 that present in experiment-1 are listed and are all allowed.
2. `1,8,2-7` or `1,8,7-2`: combination of individual and range assignment.
3. `8,1,7-2,6`: redundancy is tolerant.
## Step-2: Specify Configuration of Workflow
Run `new-configuration-file` command to initiate configuration file (YAML
format) which specify the details of CEL-Seq2 techniques the users perform.
``` bash
new-configuration-file -o /path/to/wonderful_CEL-Seq2_config.yaml
```
Example of configuration is [here](https://gitlab.com/Puriney/celseq2/blob/master/example/config.yaml).
## Step-3: Run Pipeline of `celseq2`
Examine how many tasks to be performed before actually executing the pipeline:
......@@ -106,7 +108,7 @@ Examine how many tasks to be performed before actually executing the pipeline:
celseq2 --configfile /path/to/wonderful_CEL-Seq2_config.yaml --dryrun
```
Run pipeline:
Launch pipeline:
``` bash
celseq2 --configfile /path/to/wonderful_CEL-Seq2_config.yaml
......@@ -119,10 +121,27 @@ user could run the following command to submit jobs to computing nodes. Here it
submits 10 jobs in parallel with total maximum memory 50G requested.
``` bash
celseq2 --configfile /path/to/wonderful_CEL-Seq2_config.yaml \
celseq2 --config-file /path/to/wonderful_CEL-Seq2_config.yaml \
--experiment-table /path/to/wonderful_experiment_table.txt \
--output-dir /path/to/result_dir \
-j 10 \
--cluster "qsub -cwd -j y -l h_vmem=50G" &
```
# Documents
# Result
```
expr/
├── E1
│   ├── expr.csv
│   ├── expr.h5
│   └── item-1
│      ├── expr.csv
│      └── expr.h5
└── E2
├── expr.csv
├── expr.h5
└── item-2
   ├── expr.csv
   └── expr.h5
```
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