wassermanlab / biasaway Goto Github PK
View Code? Open in Web Editor NEWLicense: GNU Lesser General Public License v3.0
License: GNU Lesser General Public License v3.0
Hi,
I am running BiasAway in a human dataset. tes_background_hsapeins.fa is coming from random fragments of 1000bp (done with bedtools). The TE_set_reference_hg38.fa is a compendium of 4million transposable elements. I get a weird error after quite a while of computation.
time python /home/jl/soft/bias_away/BiasAway.py c -b /projects/TE_stress_project/chip_seq_data/background_seqs/tes_background_hsapiens.fa -f /projects/TE_stress_project/humans/TE_set_reference_hg38.fa -r background_te_hsapiens/ > te_background_gc_matched_hsapiens.fa
/home/jl/soft/bias_away/GC_window_compo_matching.py:37: RuntimeWarning: invalid value encountered in double_scalars
return gc, min(tmp_gc), max(tmp_gc), sd, 100 * sd / gc
/home/jl/soft/bias_away/GC_window_compo_matching.py:37: RuntimeWarning: divide by zero encountered in double_scalars
return gc, min(tmp_gc), max(tmp_gc), sd, 100 * sd / gc
Killed
real 726m6.471s
user 704m29.162s
sys 4m44.320s
Is there a link from which I can download 1000bp background sequences for hg38? Thanks!
Hi, do you happen to have hg19 150bp precomputed background sequences? If not, do you have precomputed background sequences of size 150bp? Thank you!
Which genome assemblies were used for generating your mouse and human backgrounds? Thanks!
Where do the shuffled/random regions get recorded? Thanks!
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.