Comments (5)
We are working on making the scripts available. I would suggest you follow the procedure as described in the LeafCutter preprint (http://biorxiv.org/content/early/2016/03/16/044107) to qqnorm+standardize your intron ratio data, and use fastQTL(http://fastqtl.sourceforge.net/) for QTL mapping.
from leafcutter.
Thank you for your reply. There is a lot of analysis described in paragraph 6.1 of your paper so I was hoping I wouldn't have to re-create it. Any idea of when those scripts might become available? One more question, why did you decide to remove "all associations that might be caused by SNPs that overlap junction reads"? Is that because these SNPs are not sQTLs as such but mutations that happen to introduce splice donor or acceptor sites? Finally, I've come across sQTLseekeR (http://www.nature.com/articles/ncomms5698#supplementary-information) which seems like it does a similar analysis. Do you have any comments on how that compares to your analysis? Thank you very much for your time.
from leafcutter.
I'll try to make those scripts available right after US Thanksgiving. In
general, we would not remove associations where a SNP overlaps junction
reads if WASP was used to re-map reads, but we did not re-align every bam
file. In order to do a proper analysis, you must use WASP or similar
methods to remove all allelic reads that might map incorrectly or not at
all. This is time consuming and one of the reasons why I did not initially
release code for sQTL mapping: it would produce false positives if WASP was
not used.
If I recall correctly, sQTLseekeR tries to find novel isoforms, but
estimates isoform level changes, which is known to be noisy. It finds many
fewer sQTLs compared to most other methods.
Yang
On Wed, Nov 23, 2016 at 6:25 AM, Stathis [email protected] wrote:
Thank you for your reply. There is a lot of analysis described in
paragraph 6.1 of your paper so I was hoping I wouldn't have to re-create
it. Any idea of when those scripts might become available? One more
question, why did you decide to remove "all associations that might be
caused by SNPs that overlap junction reads"? Is that because these SNPs are
not sQTLs as such but mutations that happen to introduce splice donor or
acceptor sites? Finally, I've come across sQTLseekeR (
http://www.nature.com/articles/ncomms5698#supplementary-information)
which seems like it does a similar analysis. Do you have any comments on
how that compares to your analysis? Thank you very much for your time.—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
#15 (comment),
or mute the thread
https://github.com/notifications/unsubscribe-auth/AE1pieBMv6VfCxNZUwW05eSA-ey-leB7ks5rBCLAgaJpZM4K5rDB
.
from leafcutter.
Ok thank you for your advice. I'll give WASP a try in the meantime.
from leafcutter.
We've added scripts/prepare_phenotype_table.py
to process the intron counts into an appropriate format for FastQTL, including splicing PCs. There's some documentation at the end of the main README too.
from leafcutter.
Related Issues (20)
- Does Leafviz work on leafcutterMD result? HOT 3
- error in leafcutter_cluster_regtools.py
- Not reproducible results
- Redundant Splice Event Clustering HOT 1
- Confusion about Proper Input File Extension and Content
- Question about applying PCA on intron usage ratios
- example_data missing
- Bug found in hg38 annotation codes file for LeafViz HOT 1
- how to identify the alternative splicing events for differential cluster, such as ES/MXE/IR/Alt5’/Alt3’
- shinyapp leafcutter HOT 1
- enhancement HOT 2
- Behavior of -p --mincluratio: unexpectedly removing intron clusters HOT 1
- Potentially incorrect use of minclureads and minreads HOT 4
- confusion of normalization method for sQTL input date prepare HOT 1
- Alternative splicing signal on tandem duplicated genes HOT 1
- Creating co-splicing networks with leafcutter output?
- this is broken
- differential splicing with continuous independent variable
- Positive splicing events are not be detected HOT 2
- Start and end sites of junctions
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 leafcutter.