jaredslosberg / get_sra_fastqs Goto Github PK
View Code? Open in Web Editor NEWSnakemake workflow to grab raw fastqs from SRA from SRR, SRX, SRP, or PJRNA accession numbers
get_sra_fastqs's People
Contributors
Stargazers
Watchers
get_sra_fastqs's Issues
Update to also grab metadata
In addition to raw fastqs, also grab metadata for an experiment which would include things like tissue, prep, experiment/run, paired/single end... Either do this with XML parsing or find a package that already does it
XML file size limitations
using perl xpath to strip metadata from xml files crashes for SRA projects with many samples (eg SRP056477)
error message:
Ran out of memory for input buffer at /home/[...]/lib/site_perl/5.26.2/x86_64-linux-thread-multi/XML/Parser/Expat.pm line 474.
free(): invalid next size (normal)
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.