Commit db05ce4d authored by yy1533's avatar yy1533
Browse files

Merge branch 'master' into ST

parents d85c2668 364c1657
# List of supported techniques
Though `celseq2` is dedicated to process CEL-Seq2 sequencing data, it is also
compatible to data generated in following contexts, because of the similar design
principles of the UMI and cell barcodes.
1. Spatial transcriptome data. `celseq2` works similar to
[st_pipeline](https://github.com/SpatialTranscriptomicsResearch/st_pipeline),
except that `celseq2` uses Bowtie2 for aligment while `st_pipeline` uses STAR.
\ No newline at end of file
# FAQ
:question: Can `celseq2` process data from other scRNA-seq methods? For example,
spatial transcriptome?
:star: See [List of supported techniques](about/support_others.md#).
# Run pipeline
Examine how many tasks to be performed before actually executing the pipeline:
Learn about how it is easy to launch pipeline in all the ways users want.
---
The design of how to launch the pipeline reflects our philosophy about pipeline
and the effort to realize superb user experience.
## Dry-run
Set `--dryrun` flag to examine how many scheduled tasks to be performed before
actually executing the pipeline. Here one task could be aligning one FASTQ file,
or counting UMI from one SAM alignment file.
``` bash
celseq2 --config-file /path/to/wonderful_CEL-Seq2_config.yaml \
......@@ -8,7 +20,10 @@ celseq2 --config-file /path/to/wonderful_CEL-Seq2_config.yaml \
--dryrun
```
Launch pipeline in the computing node which performs 10 tasks in parallel.
## Launch pipeline to run parallel tasks
Set `-j 10` to launch pipeline with 10 tasks executed in parallel. This can run
on either the computing node or your own computer.
``` bash
celseq2 --config-file /path/to/wonderful_CEL-Seq2_config.yaml \
......@@ -17,11 +32,15 @@ celseq2 --config-file /path/to/wonderful_CEL-Seq2_config.yaml \
-j 10
```
## Submit tasks to server
Alternatively, 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 50G of memory requested by each.
submitting jobs to cluster, as `celseq2` is built on top of
[`snakemake`](https://bioconda.github.io/recipes/snakemake/README.html) which is
a powerful workflow management framework.
For example, user could run the following command to submit jobs to computing
nodes. Here it submits 10 jobs in parallel with 50G of memory requested by each.
``` bash
celseq2 --config-file /path/to/wonderful_CEL-Seq2_config.yaml \
......
# Storage Management
Learn how to reduce storage while maintaing the results.
---
To reduce the storage of project, it is suggested to get rid of intermediate
files, in particular FASTQ and SAM files.
Remove all FASTQ and SAM files generated by `celseq2`.
```
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 clean_FQ_SAM
```
Alternatively, user can gzip FASTQ and convert SAM to BAM:
```
celseq2-slim --project-dir /path/to/result_dir --dryrun
celseq2-slim --project-dir /path/to/result_dir
```
\ No newline at end of file
......@@ -35,8 +35,11 @@ pages:
- 'Setup configuration': 'user_guide/setup_config.md'
- 'Specify experiment table': 'user_guide/experiment_table.md'
- 'Launch pipeline': 'user_guide/launch_pipeline.md'
- 'Storage management': 'user_guide/storage.md'
- About:
- 'Reproducibility': 'about/reproducibility.md'
- 'Performance': 'about/performance.md'
- 'User Experience': 'about/user_friendly.md'
- 'Release Note': 'about/release_note.md'
- 'User experience': 'about/user_friendly.md'
- 'Support other methods': 'about/support_others.md'
- 'Release note': 'about/release_note.md'
- FAQ: 'faq.md'
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment