Commit d79f32d1 authored by yy1533's avatar yy1533
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🍺 📖 release quick-start of readme

parent 677e4244
......@@ -61,9 +61,9 @@ to allow assessment on reproducibility or possible batch effect.
## Step-1: Define Experiment Table
Run `new-experiment-table` command to initiate table file (space/tab separated
file) of the experiment design.
file) to specify the experiment layout.
```bash
``` bash
new-experiment-table -o /path/to/wonderful_experiment_table.txt
```
......@@ -97,17 +97,41 @@ indexed from 1 to 8 that present in experiment-1 are listed and are all allowed.
## Step-2: Specify Configuration of Workflow
Run `new-configuration-file` command to initiate configuration file
(YAML format) of CEL-Seq2.
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: Running `celseq2`
## Step-3: Run Pipeline of `celseq2`
# Documents
Examine how many tasks to be performed before actually executing the pipeline:
``` bash
celseq2 --configfile /path/to/wonderful_CEL-Seq2_config.yaml --dryrun
```
Run pipeline:
``` bash
celseq2 --configfile /path/to/wonderful_CEL-Seq2_config.yaml
```
In addition, it is straightforward to run the pipeline of `celseq2` by
submitting jobs to cluster, as `celseq2` is built on top of `snakemake` which is
a powerful workflow management framework. For example, in login node on server,
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 \
-j 10 \
--cluster "qsub -cwd -j y -l h_vmem=50G" &
```
# Documents
......@@ -19,9 +19,6 @@ BOWTIE2: '/local/apps/bowtie2/2.3.1/bowtie2'
## Annotations ##
GFF: '/ifs/data/yanailab/refs/danio_rerio/danRer10_87/gtf/Danio_rerio.GRCz10.87.gtf.gz'
## Cell Barcodes ID
#bc_ids_used: '1,2,3,4-5'
## Demultiplexing ##
FASTQ_QUAL_MIN_OF_BC: 10
CUT_LENGTH: 35
......
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