Commit 6584e38b authored by Wai Yi Leung's avatar Wai Yi Leung

Setup the documentation for tinycap

parent a2af9e51
# Introduction
``TinyCap`` is an analysis pipeline meant the process smallRNA captures.
# Starting the pipeline
biopet pipelines tinycap [options] \
-config `<path-to>/settings_tinycap.json`
-config `<path-to>/sample_sheet.json` \
-l DEBUG \
-qsub \
-jobParaEnv BWA \
-run
# Example
Note that one should first create the appropriate [configs](../general/config.md).
The pipeline specific (minimum) config looks like:
```
{
"output_dir": "<path-to>/outputdirectory",
"reference_name": "GRCh38",
"species": "H.sapiens",
"annotation_gff": "<path-to>/data/annotation/mirbase-21-hsa.gff3",
"annotation_refflat": "<path-to>/data/annotation/ucsc_ensembl_83_38.refFlat",
"annotation_gtf": "<path-to>/data/annotation/ucsc_ensembl_83_38.gtf"
}
```
One can specify other options such as: `bowtie` (alignment) options, clipping and trimming options `sickle` and `cutadapt`.
Example:
```
"bowtie": {
"chunkmbs": 256, # this is a performance option, keep it high (256) as many alternative alignments are possible
"seedmms": 3,
"seedlen": 25,
"k": 5, # take and report best 5 alignments
"best": true # sort by best hit
},
"sickle": {
"lengthThreshold": 8 # minimum length to keep after trimming
},
"cutadapt": {
"error_rate": 0.2, # recommended: 0.2, allow more mismatches in adapter to be clipped of (ratio)
"minimum_length": 8, # minimum length to keep after clipping, setting lower will cause multiple alignments afterwards
"q": 30, # minimum quality over the read after the clipping in order to keep and report the read
"default_clip_mode": "both", # clip from: front/end/both (5'/3'/both). Depending on the protocol. Setting `both` makes clipping take more time, but is safest to do on short sequences such as smallRNA.
"times": 2 # in cases of chimera reads/adapters, how many times should cutadapt try to remove am adapter-sequence
)
```
# Testcase A
# Examine results
## Result files
## Best practice
# References
......@@ -16,6 +16,7 @@ pages:
- Mapping (Alignment): 'pipelines/mapping.md'
- Sage: 'pipelines/sage.md'
- Shiva (variantcalling): 'pipelines/shiva.md'
- TinyCap (smallRNA): 'pipelines/tinycap.md'
- Toucan (Annotation): 'pipelines/toucan.md'
- Tools:
- SamplesTsvToJson: 'tools/SamplesTsvToJson.md'
......
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