Comments (2)
Hi, @mstemmer,
Quite a few things happen under the hood.
First, bustools whitelist
is run, which detects a barcode count threshold based on the first 200 to 100200 BUS records and generates a whitelist of barcodes that will be considered true "cells." These barcodes are in the filter_barcodes.txt
file that is generated in the output directory.
Then, bustools correct
is run with the newly generated whitelist to correct barcodes with single point mutations (hamming distance 1). It also filters for barcodes in the whitelist.
Finally, bustools count
is run to generate a cells by gene matrix containing gene counts.
You can read what each of these commands do in more detail here: https://bustools.github.io/manual
from kb_python.
This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days
from kb_python.
Related Issues (20)
- SmartSeq3 Demultiplexed Fastq files HOT 4
- kb-python version 0.28.2 giving problems on m1 mac HOT 6
- Is kb-python capable of processing many samples in one command? HOT 2
- --umi-gene no longer supported in kb count? HOT 2
- Containerized kb can choose the wrong binary HOT 1
- How to run RNA velocity analysis (La Manno) on BAM files HOT 4
- kb-python processing significantly less reads HOT 6
- Crosspost from kallistobustools: kb count error with CSP reads HOT 21
- Running kb count with a single FASTQ file HOT 4
- kb count - joint vs individual sample processing for RNA velocity analysis HOT 2
- kb ref can't handle blanks in path arguments HOT 2
- Naive collapsing of UMIs in SS3xpress data? HOT 6
- No reads pseudoaligned in 10XV1 chemistry HOT 6
- Usage of f1 and f2 parameters in kb ref and count HOT 2
- Changed barcodes from the kb-python count HOT 2
- Issue obtaining unaligned reads HOT 3
- Kb count command stuck on bustools count step HOT 5
- kb-python for MARS-seq HOT 1
- Syntax for 3-reads, paired end technology? HOT 3
- Whitelist for SMARTSEQ2 technology HOT 6
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 kb_python.