Commit 807482be authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge branch 'fix-smallrna-defaultsettings' into 'develop'

Fix smallrna defaultsettings

Change settings to validated settings (by Peter Bram)

See merge request !424
parents a98db543 a11fe236
......@@ -55,35 +55,23 @@ One can specify other options such as: `bowtie` (alignment) options, clipping an
"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
"k": 3, # take and report best 3 alignments
"best": true, # sort by best hit,
"strata" true # select from best strata
},
"sickle": {
"lengthThreshold": 8 # minimum length to keep after trimming
"lengthThreshold": 15 # 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
"error_rate": 0.1, # recommended: 0.1, allow more mismatches in adapter to be clipped of (ratio)
"minimum_length": 15, # 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
"default_clip_mode": "3", # clip from: front/end/both (5'/3'/both). Depending on the protocol.
"times": 1, # in cases of chimera reads/adapters, how many times should cutadapt try to remove am adapter-sequence
"ignore_fastqc_adapters": true # by default ignore the detected adapters by FastQC. These tend to give false positive hits for smallRNA projects.
}
```
The settings above is quite strict and aggressive on the clipping with `cutadapt`. By default the option `sensitiveAdapterSearch` is turned on in the TinyCap pipeline:
```json
"fastqc": {
"sensitiveAdapterSearch": true
}
```
This setting is turned on to enable aggressive adapter trimming. e.g. found (partial) adapters in `FastQC`
are all used in `Cutadapt`. Depending on the sequencing technique and sample preparation, e.g. short
sequences (76bp - 100bp). Turning of this option will still produce sensible results.
## Examine results
### Result files
......
......@@ -64,22 +64,24 @@ class TinyCap(val root: Configurable) extends QScript
"bowtie" -> Map(
"chunkmbs" -> 256,
"seedmms" -> 3,
"seedlen" -> 25,
"k" -> 5,
"best" -> true
"seedlen" -> 28,
"k" -> 3,
"best" -> true,
"strata" -> true
),
"sickle" -> Map(
"lengthThreshold" -> 15
),
"fastqc" -> Map(
"sensitiveAdapterSearch" -> true
"sensitiveAdapterSearch" -> false
),
"cutadapt" -> Map(
"error_rate" -> 0.2,
"error_rate" -> 0.1,
"minimum_length" -> 15,
"q" -> 30,
"default_clip_mode" -> "both",
"times" -> 2
"default_clip_mode" -> "3",
"times" -> 1,
"ignore_fastqc_adapters" -> true
)
)
......
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