Comments (2)
Hi Matt and Jacqueline,
I have tried Annelida and Cnidaria at 590 bp, 620 bp, and 650 bp. I found that the impacts of trimming length were modest. While p-values were different, the overall conclusions that would be drawn were the same. (Also, p-values have to be interpreted with caution for small sample sizes anyhow.) The impacts upon the average and median relative distances were also modest.
Given the modest impacts, I think our original decision of a 620 bp length was reasonable. This trims ~20 bp off each end (in relation to the total region amplified between the primers). In my experience editing chromatograms, frequently approximately that length is only represented by one of two trace files, even with bidirectional sequencing. Also, Taryn Athey's MSc thesis shows concentrations of low frequency variants at the ends (which are more likely errors), further justifying the use of some trimming.
I do think that some trimming (rather than using the 658 bp) is reasonable. I have found that, in contrast to trimming length, alignment errors can make a difference. Sometimes, when the signal becomes weak near the end of a trace file, an EXTRA nucleotide is erroneously called. When this happens in the forward chromatogram, there may not be enough length left in the contig sequence for a stop codon to crop up (which would block a sequence from getting a BIN assignment). So, in order to use a stiff gap opening penalty (resulting in a better alignment Cnidaria, at least - i.e. maintaining correct reading frame and amino acid translation), we would want to trim off such cases.
So, I suggest 620 bp. Any comments are welcome!
If the cloud-based runs go well and are very fast, we could consider re-running the analyses at an alternative length for verification that the results were minimal upon the results, using a much larger dataset (e.g. large phylum).
Best wishes,
Sally
from evolutionary-rates-analysis-pipeline.
I will close this issue, as we have moved the topic to the thread discussing the final filtering and trimming settings.
Best wishes,
Sally
from evolutionary-rates-analysis-pipeline.
Related Issues (20)
- Using Cloud Computing with RStudio HOT 88
- Discussion - Running Cnidaria HOT 6
- Question about filtering by sequence length HOT 17
- Sally's next tasks HOT 22
- New Mollusca Results HOT 14
- Alignment of mite group Mesostigmata HOT 25
- R Style Guide HOT 16
- Model test HOT 4
- Update to Pipeline and New Branch HOT 3
- Median latitude HOT 10
- Jacqueline got an error line 569 of Annelida branch HOT 10
- Error on line 1572 of Annelida branch HOT 5
- Very minor edits! HOT 5
- Identify weird sequences HOT 9
- Ideas to consider for V2 HOT 16
- New Results Thread HOT 73
- Sister vs. Phylo pipeline comparison HOT 3
- Map Figures HOT 20
- Matt - task list HOT 9
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 evolutionary-rates-analysis-pipeline.