Comments (2)
acesnik
commented on September 24, 2024
Alternatively, allow combining fastqs after downloading SRAs.
from spritz.
acesnik
commented on September 24, 2024
There is a tradeoff here:
- Combining read files before the whole analysis is simpler to code and manage
- But processing the read files separately can give useful information regarding the consistency of variant detection. This is especially important for splice variants. We could use rMATs, which I've already started wrapping or JUM, which outperforms rMATS in number of interesting ways, to find which splice junctions are consistent between tech reps. This is an idea that comes from here https://www.biorxiv.org/content/biorxiv/early/2018/07/27/372995.full.pdf.
from spritz.
Related Issues (20)
- Worflow processing time HOT 9
- Missing input files for rule fastp_fq HOT 1
- Still running after five days of computation HOT 4
- (1) "Error waiting for container: invalid character 'u' looking for beginning of value" (2) "Could not execute because the application was not found or a compatible .NET SDK is not installed." HOT 61
- Same issue as #199 with updated mzLib HOT 8
- gatk MarkDuplicates Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded HOT 11
- Spritz crashing after command line execution (Ubuntu). Step 10. HOT 14
- Option to generate separate databases for each input
- Simplifying version checks HOT 1
- Integration into snakepipes HOT 1
- Slight discrepancy in number of targets and decoys in `withdecoys.fasta` after mzLib decoy generation
- FragPipe-ready fasta headers and redundancy reduction HOT 5
- Conda/dotnet not properly detecting openssl within minimamba docker container; probable conda issue HOT 3
- Using Arabidopsis sequences for tests instead of yeast HOT 1
- Update uniprot URLs to rest.uniprot from legacy.uniprot
- Error response from daemon: No such container: spritz-615926720 HOT 6
- Error in rule reorder_genome_fasta HOT 3
- Error in rule make_gene_quant_dataframe_ref HOT 14
- Enable running Spritz with singularity
- Error in rule setup_transfer_mods HOT 7
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 spritz.