Commit e1042d1d authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Change some wordings..

parent f79d1fa5
......@@ -12,7 +12,7 @@ The sample config should be in [__JSON__](http://www.json.org/) or [__YAML__](ht
#### Example sample config
###### yaml:
###### YAML:
``` yaml
output_dir: /home/user/myoutputdir
......@@ -24,7 +24,7 @@ samples:
R2: R2.fastq.gz
```
###### json:
###### JSON:
``` json
{
......
......@@ -2,10 +2,10 @@
## Introduction
``TinyCap`` is an analysis pipeline meant the process smallRNA captures. We use a fixed aligner in this pipeline: `bowtie` .
``TinyCap`` is an analysis pipeline meant to process smallRNA captures. We use a fixed aligner in this pipeline: `bowtie` .
By default, we allow one fragment to align up to 5 different locations on the genome. In most of the cases, the shorter
the sequence, the less 'unique' the pattern is. Multiple "best" alignments is in these cases possible.
To not create a 'first-occurence found and align-to' bias towards the reference genome, we allow the aligner
the sequence, the less 'unique' the pattern is. Multiple **"best"** alignments is in these cases possible.
To avoid **'first-occurence found and align-to'** bias towards the reference genome, we allow the aligner
to report more alignment positions.
After alignment, `htseq-count` is responsible for the quantification of transcripts.
......@@ -46,10 +46,10 @@ The pipeline specific (minimum) config looks like:
}
```
One can specify other options such as: `bowtie` (alignment) options, clipping and trimming options `sickle` and `cutadapt`.
### Example config:
### Advanced config:
One can specify other options such as: `bowtie` (alignment) options, clipping and trimming options `sickle` and `cutadapt`.
```json
"bowtie": {
"chunkmbs": 256, # this is a performance option, keep it high (256) as many alternative alignments are possible
......
Supports Markdown
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