Comments (2)
- Does seq2science need to be fully rerun? No, seq2science can continue from the last possible point, as to save compute. There is a minor "problem", in that seq2science deletes some files to not save too much unnecessary stuff (called temp files). For your case, seq2science removes the trimmed fastqs after it is done with them, because otherwise it will keep both the raw fastqs as the trimmed ones. That's a waste of space! You can turn off the removal of temp files with
--snakemakeOptions notemp=True
. Make sure to check if this works as expected with--dryrun
, because might just delete some files you wanted to keep after all... - Are the results stored in the same spot? Yes and no... The results of the quantifier are stored in the folder specific for the quantifier, so they won't overlap. The downstream results, for instance, the differential analysis, is stored in the same deseq folder. So those will be overwritten
So it is possible indeed. If you don't have too many samples then I think it is the easiest and least error prone to just run them in separate folders. However if you have a lot of samples, or are limited by compute/storage/time then you can reuse some of the seq2science output.
from seq2science.
Adding to Maarten's asnwer: you can change the counts_dir
and/or final_bam_dir
in the config. That way, the final output is kept separately. Check out all configurable options.
from seq2science.
Related Issues (20)
- BUG: download_fastq report error HOT 4
- BUG: [config.yaml error] HOT 15
- Combining STAR and Salmon HOT 5
- STAR 2-pass alignment HOT 1
- Q: [DEG analysis contrast] HOT 1
- BUG: chipseeker is broken (again)
- FR: [DEG by Salmon]
- FR: python/scanpy interoperability for single cell?
- FR: single cell auto detection if droplet or cell based barcodes?
- BUG: qc_scRNA rules dont use params, so rerunning doesn't work
- FR: single cell RNA filtering
- Issue with Chip-seq pipeline: jobid: 27: one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode! HOT 8
- Q: Stuck with initialisation of a workflow (atac-seq) HOT 13
- BUG: Problem with the Initiation HOT 6
- FR: Use temporary directories for sra and temporary fastq files HOT 14
- BUG: Incorrect SRA files (RNA-seq) HOT 1
- BUG: [scATAC-seq successful run but bam file and snap object are missing cell barcodes] HOT 6
- FR: don't crash when no differential genes are found HOT 4
- BUG: latest numpy version and IDR inconsistency 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 seq2science.