Comments (2)
What are your read lengths?
So the default method is to merge reads with usearch, if a pair does not merge then the forward read is rescued. I have typically been able to merge ~90-95% of reads - we have used 2 x 300 using a double indexed strategy and default illumina sequencing primers.
Per the code, the merging command for usearch/vsearch is here, you'll note that I have some somewhat customized calls to usearch, this is actually to increase the number of reads that are merged.
https://github.com/nextgenusfs/amptk/blob/master/amptk/amptklib.py#L1180-L1183
As of right now there isn't the ability to customize the merging command in AMPtk. I guess my thought would be to try on a single sample several different parameters to usearch/vsearch and see if you can increase the merging. My guess might be that you have low quality reverse reads and they are getting clipped off and therefore not merged. If the quality score is below 5 it will get truncated before the alignment step. So you can also check your quality with some like fastqc or there are many other ways, but basically look at the quality scores near the 3' end of the reverse reads -- this is typically where some MiSeq runs fail (especially with 2 x 300). If you have low quality reverse reads, you might want to just use the forward reads, or allow the merging as above, but set your trim length to less than your read length, i.e. if you have 250 bp reads, then I'd set it to something like 230-240 so you keep as much data as you can.
from amptk.
Thanks for the quick reply
Our reads are also 2 x 300/double index/MiSeq
We do have low Q around the R2 3'. Maybe adapters read-through too.
I hope using forwards only do the trick
I'll test your suggestion on trim and show the counts
Thanks again
from amptk.
Related Issues (20)
- Support Python 3.8 onwards HOT 3
- SyntaxError in "duplicate ID in mapping file: XXX, exiting"
- Default for -p, --index_bleed documented as 0.005 HOT 1
- Typo "Bjerkandara adusta" --> "Bjerkandera adusta" HOT 1
- Missing species names in amptk_mock1.fa HOT 3
- Missing final new line in amptk_mock1.fa and amptk_synmock.fa HOT 2
- Inconsistent primer trimming sequence in amptk_mock*.fa HOT 5
- Matching MockA, MockB1 and MockB2 to FASTQ filenames HOT 2
- platform.linux_distribution is removed since Python 3.8 HOT 1
- Species names in amptk_mock2.fa and amptk_mock3.fa vs Figure 4
- new users cannot install amptk properly, please help HOT 3
- unoise3 clustering HOT 5
- Problem with TypeError during AMPtk cluster HOT 11
- Saw you started some prelim ONT methods HOT 2
- Problematic unoise3 implementation with VSEARCH HOT 13
- Issue installing AMPtk (Mac OS - M1 chip) HOT 2
- getting NoneType vs int error in clustering step
- Error when run quick start HOT 7
- usearch9 not found when generate UTAX database
- VSEARCH error on amptk -filter step
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 amptk.