Comments (7)
Hi @fancyge, thanks for the enhancement suggestion. For processing kraken output you have already the option to taking compressed files (see Kraken: use of compressed files). Which output files are you thinking of? Thanks.
from recentrifuge.
Hi, thanks a lot for the quick response! I have already got the centrifuge classification files and want to run rextract to filter the reads. I noticed that rextract can only take fastq file but will go wrong with "fastq.gz" file. I prefer "fastq.gz" for storage saving purpose.
Thank you.
from recentrifuge.
OK, I see, it is about rextract
. The issue #28 is also an enhancement suggestion, so I will probably address both of them soon.
About the -i
option, you have to prepend any taxid to include with such a flag. In your case:
rextract -f my_classification_results.txt multiple -i 9606 -i 452 -1 R1.fq -2 R2.fq
from recentrifuge.
Thanks! Hope to see it soon! Quite useful tools!
By the way, do you have an idea what score (-y) I should feed to rextract for filtering centrifuge results? I have 150bp fastq files from illumina sequencing.
from recentrifuge.
I just added some commands to make it possible to take&output zipped fastq files. It might not be ideal but can be used at the moment. Thanks.
from recentrifuge.
By the way, do you have an idea what score (-y) I should feed to rextract for filtering centrifuge results? I have 150bp fastq files from illumina sequencing.
My recommendation is to avoid too low minscore
(-y
flag also) values to filter sequences with low scores. Also, if you have control sequences, you may want to lower ctrlminscore
(-z
flag also) to have more sequences in the controls and thus more sequences removed after the robust control removal algorithm. So, --minscore 35 and --ctrlminscore 25 could be good values to start with.
from recentrifuge.
I just added some commands to make it possible to take&output zipped fastq files. It might not be ideal but can be used at the moment. Thanks.
Thanks! If you open a PR I'd happy to check it and include it in the master branch.
from recentrifuge.
Related Issues (20)
- ZeroDivisionError HOT 2
- Compatibility with Ganon? HOT 5
- rextract: ZeroDivisionError HOT 3
- -k for multiple directories of .krk files? HOT 3
- Contamination removal help and too large HTML files HOT 11
- definition of contaminat level for removal? HOT 1
- interpreting log file for contamination removal HOT 3
- abundance table as output HOT 1
- Enhancement: provide control samples in a different directory
- (question) produced output HOT 1
- Score understanding HOT 1
- refasplit output files with non-padded zeros
- Rextract from Kraken2 output HOT 1
- float deprecated in numpy 1.24 HOT 1
- Issue with nodes/names missing unclassified readID (0) HOT 1
- ImportError: cannot import name 'SequentialSequenceWriter' from 'Bio.SeqIO.Interfaces' HOT 9
- OverflowError when trying passing centrifuge input test HOT 3
- Building nt database - no multithreading at centrifuge-build step HOT 5
- taxonomy files for common 16S datasets?
- Error code 13? 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 recentrifuge.