Comments (10)
Could you please send me your bed file for this sample along with a BAM header (or something that lists the reference sequences and lengths)?
from abra.
I am not sure how to attach text file here. I tried replying to your email but it failed. Let me know where should i send you those files.
from abra.
Please send to: lmose at unc dot edu
from abra.
Thanks. You've uncovered a bug in our handling of contigs mapping near the ends of chromosomes. I've committed a fix (lightly tested so far) to the head. Unfortunately, the head has some other recent commits that should undergo additional testing. I expect to have a release including this change available sometime next week.
If you need this urgently, applying this same commit to a previous release should work fine. I can help with that if needed.
Here's the change:
b0a2e67
For your specific test case, the problematic contig appears to be mapping near the end of chromosome MT.
Lastly, I noticed from your logs that you are passing in kmer values on the command line. Abra now can automatically calculate appropriate kmer sizes on a per region basis. We see improved results using this approach. Just omit the kmer param if you'd like to give it a try.
from abra.
Cool Thanks for your quick reply and appreciate the quick fix. I will wait for you to release the new code. Do you have a summary of improvements for your next release. Also do you know if we can make this code work for Amplicon Based datasets where they have fixed start and stop sites.
I know about the automatic size selection. I was testing this for out next release in the pipeline. But will make sure we test it without the k-mer values once you upload the new code.
JUST FYI:
Also We like you thank you for this amazing tool, one of my summer high school student evaluated it last year and here is his poster:
http://www.slideshare.net/rshah7/final-posterhopp
from abra.
Wow, thanks for the feedback!
We don't typically use the fixed start/stop amplicon datasets you've described. If you have a test set that you are able to share I'd be happy to take a look. I am a bit skeptical though as the assembly generally works better with some read complexity across the variant. Are you using this amplicon method for discovery or for validation?
Will put together notes describing the changes in next week's release.
from abra.
Thanks for working on this. The amplicon data we are using that for discovery of know variation and we are missing some. I agree due to no read complexity it will be hard to do this. I will mail you the scrubbed data and we can go from there.
Thanks,
Ronak
from abra.
Sorry, but the forthcoming release is going to have to slide to next week.
from abra.
OK, thanks for keeping me in the loop. I am currently trying to gather scrubbed amplicon based data for testing, will update you once I have that.
from abra.
The original bug reported should be resolved in v0.91. Please let me know if you run into any more problems.
from abra.
Related Issues (20)
- Excessive run time HOT 2
- [fwrite] Remote I/O error HOT 5
- polyA/polyT/lowcomplexity region realignments for single ended reads HOT 3
- Exception in thread Error HOT 2
- Error in Cadabra HOT 4
- [Request] Replace System.out.print* statements with System.err.print* for stream compatibility HOT 3
- Amplicon data HOT 5
- xlC compatibility - C++ STL referenced in .c files HOT 4
- hidden dependency on bwa mem HOT 2
- Abra error HOT 2
- Change header in bam HOT 1
- Is YA tag deterministic? HOT 4
- Abra will realign duplicates? HOT 5
- Testing practices HOT 2
- Abra processes unique reads? HOT 2
- Is it possible to get the assembled contig? HOT 2
- No contigs assembled: no space left on device HOT 1
- abra2 error java.lang.NumberFormatException HOT 3
- build issue
- java.lang.IllegalStateException
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 abra.