Comments (10)
Which changes you mean?
from snakepipes.
Any updates present in current develop, like for example the trimming option were different between scRNAaseq and other workflows
from snakepipes.
the slight differing trimming option was intentionally, as poly-A trimming is "easier" with cutadapt, therefore scRNA-seq supports only cutadapt right now....but I can change this for consistency
from snakepipes.
@steffenheyne feel free to close this if you think it's done
from snakepipes.
Isn't cutadapt
the default trimmer in the other workflows already? I wouldn't oppose getting rid of Trim Galore all together, since cutadapt is vastly faster.
from snakepipes.
yes, cutadapt is default everywhere...and as trimgalore is just a "convenience" wrapper around cutadapt, I'm fine getting rid of trimgalore.
more general aspect: I'm just always a bit afraid that we miss/might use the right adapter/primer sequence as there are eg slight diff. between small RNA-seq and other protocols, here trimGalore has some autodetect function, but also I'm not sure how good this is actually working etc...
should we make adapter sequence configureable via defaults.yaml?
from snakepipes.
currently we just use always "AGATCGGAAGAGC"
from snakepipes.
We could make that configurable I suppose. I actually want to add a --detect
option to cutadapt (I looked into making Trim Galore multithreading...but that'd be absurdly complicated). I think Trim Galore does an OK job for the most part with adapter detection, but of course if you know what the adapter is then that'll always be the most reliable. The WGBS pipeline has two different adapter sequences built in, so one can instead trim with Nextera adapters if needed. Maybe that's the way to go, since we don't currently support sRNA-seq.
from snakepipes.
Yah if cutadapt rule can be adopted for multiple adaptor types, I would also vote to get rid of trim-galore
from snakepipes.
see now here
#151
from snakepipes.
Related Issues (20)
- plotFinger fails due to insaficient wall time HOT 6
- [Question] where to find the exact command issued? HOT 2
- [Request] looping inputs for multiple ChIP-seq comparisons HOT 1
- allow user to specify mincount for filtering windows for DB with CSAW
- snakePipes createEnvs fails HOT 1
- human reference genome, no_alt and PARY HOT 2
- MACS3 in pipeline HOT 2
- error while creating the environment using the git devel HOT 1
- error in samtools sort HOT 3
- issue with multiqc HOT 4
- filter_reads in DNAmapping pipeline doesnt do the filtering HOT 3
- predictChIPDict for samples without input HOT 1
- MACS2_peak_qc HOT 2
- pairtools - todos
- setting_up - documentation 3.0.0 HOT 1
- conda-recipe - 3.0.0
- illegal regex - 3.0.0 HOT 3
- logs - 3.0.0 HOT 1
- smk profile checks - 3.0.0
- graphviz - DAG plotting
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 snakepipes.