Comments (3)
@Colorstorm I'm still v busy with cluster setup + teaching, so if you get a chance to look at this then please have a go (new branch). cheers
from wochenende.
Which tags to use ?
Minimap: NM:i:626
ngmlr: NM:i:493
bamutil - mismatch threshold (for read end clipping, set to 0.10 = 10% bases being mismatches). Works on BAMs
https://genome.sph.umich.edu/wiki/BamUtil:_filter
bamtools
Save this file and use as the -script parameter
bamtools filter json (must this be dyn created to get NM per read length ? for each read ?Unworkable ...
#short reads?
{
"mapQuality" : ">30",
"tag" : "NM:<4"
}
#long reads?
{
"mapQuality" : ">30",
"tag" : "NM:<100"
}
# all reads?
{
"mapQuality" : ">30",
"tag" : "NM:< READLENGTH/10"
}
from wochenende.
This has been implemented with bamtools (avoids multiple inefficient steps saving and merging BAMs), but is NOT adapted for read length (i.e. long reads) but is fixed for all read lengths.
Before:
cat sample_metagen_R1.s.bam.txt.filt.sort.csv
1_CP020566_1_Veillonella_atypica_strain_OK5_chromosome__complete_genome_BAC 2071952 136 0
1_CP023863_1_Prevotella_jejuni_strain_CD3_33_chromosome_I__complete_sequence_BAC 2204592 98 0
1_CP001721_1_Atopobium_parvulum_DSM_20469__complete_genome_BAC 1543805 44 0
1_CP024698_1_Fusobacterium_periodonticum_strain_KCOM_1283_chromosome__complete_genome_BAC 2222370 30 0
1_CP012068_1_Eubacterium_sulci_ATCC_35585__complete_genome_BAC 1739380 26 0
1_CP002122_1_Prevotella_melaninogenica_ATCC_25845_chromosome_I__complete_sequence_BAC 1796408 22 0
After (removing those with >=250 mismatches):
cat sample_metagen_R1.s.mq30.mm.bam.txt.filt.sort.csv
1_CP020566_1_Veillonella_atypica_strain_OK5_chromosome__complete_genome_BAC 2071952 118 0
1_CP023863_1_Prevotella_jejuni_strain_CD3_33_chromosome_I__complete_sequence_BAC 2204592 88 0
1_CP001721_1_Atopobium_parvulum_DSM_20469__complete_genome_BAC 1543805 32 0
1_CP024698_1_Fusobacterium_periodonticum_strain_KCOM_1283_chromosome__complete_genome_BAC 2222370 24 0
from wochenende.
Related Issues (20)
- growth rate problems HOT 3
- growth rate - exclude 1,2,3,4 etc HOT 1
- Trial tiebrush instead of mapping quality MQ
- file names too long HOT 2
- create optional cleanup script, especially for reporting. HOT 5
- missing modules - pandas, lmfit HOT 2
- postprocess - add bash args for each stage HOT 1
- Update viruses bed in extract, with new cold viruses HOT 1
- use fastp as about twice as fast as fastqc - test
- graalvm trial - eliminate python java and R dependencies in one polyglot jdk dist
- upgrade minimap2
- wochenende_postprocess -a HOT 7
- bbsplit attempt
- Update included raspir HOT 1
- reporting errors
- wochenende_postprocess raspir error HOT 1
- remove alignerboost code
- Not able to find file named "adapters_solid.fa" HOT 2
- Not able to find "AlignerBoost.jar" on internet . HOT 4
- Definition of long and short read in wochenende HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from wochenende.