Comments (15)
Yes. Our group is developing another package to support additional HLA genes. I will let you know once it is finished.
from spechla.
If the short reads cannot afford enough phase information, SpecHLA will use HLA database, genotype frequency, and pedigree information to phase the variants.
from spechla.
Great suggestion. We do have some code to extract the sequence of HLA genes from the diploid assembly. I will update SpecHLA to support typing from diploid assembly as soon as possible.
from spechla.
Hello, now SpecHLA does not support DRB3 and DRB5.
from spechla.
Do you have any plans to make SpecHLA support additional HLAs?
from spechla.
How does the SpecHLA phase the variants when only short reads are used? Thanks
from spechla.
It would be great if the next release could type HLA using diploid assembly. Thanks
from spechla.
Hello,
Thanks for the valuable suggestion. As suggested, we added a module to support HLA typing from diploid assemblies (typing_from_assembly.py
). Please see the changes in SpecHLA v1.0.3 or the latest commit.
from spechla.
Yes. Our group is developing another package to support additional HLA genes. I will let you know once it is finished.
Hello, shuai,
Are there any other tools can work for long read HLA typing ( nanopore sequencing) ?
if we just add DRB3/4/5 imgt sequence into SpecHLA db , SpeckHLA can detect accurately DRB3/4/5 allele ?
Expecting your reply !
thanks .
from spechla.
Hello,
Sorry for the delayed update. If you add DRB3/4/5 imgt sequence into SpecHLA db, it still needs some revisions in the scripts. I believe it will work well after some adjustments. I wonder do you have any benchmark data (with real data and ground truth)? With real benchmark data, we can add this function quickly.
Also, as I know HLA*LA also can work with nanopore sequencing data. But it might require too many computational resources. You can have a try on it.
Best,
Shuai
from spechla.
Hello, Sorry for the delayed update. If you add DRB3/4/5 imgt sequence into SpecHLA db, it still needs some revisions in the scripts. I believe it will work well after some adjustments. I wonder do you have any benchmark data (with real data and ground truth)? With real benchmark data, we can add this function quickly.
Also, as I know HLA*LA also can work with nanopore sequencing data. But it might require too many computational resources. You can have a try on it.
Best, Shuai
Yeah, I have got the benchmark data for A,B,C ,DRB1, DQA1,DQB1, DPA1, DPB1, DRB3/4/5 , that's why I hope you nice guy can support DRB3/4/5 as soon as possible .
could you update specHLA to support DRB3/4/5 this week ?
Thank you very much !!!
from spechla.
So great! We will update it very soon. This week is a little challenging but I believe we can finish it next week. Could you please send us the benchmark data, so that we can start to adjust the parameters.
from spechla.
So great! We will update it very soon. This week is a little challenging but I believe we can finish it next week. Could you please send us the benchmark data, so that we can start to adjust the parameters.
well, what is your email address ?
from spechla.
Thanks. My email is [email protected]
from spechla.
Thanks. My email is [email protected]
have sent my email , please check that ,thanks
from spechla.
Related Issues (20)
- ExtractHLAread.sh HOT 5
- ExtractHLAread.sh syntax errors. HOT 4
- MICA and MICB HOT 3
- Identify somatic HLA mutation from SpecHLA HOT 6
- Performace among Novoalign V4, V3 and Bowtie2 in read-binning step HOT 2
- HLA typing only based on long-read RNA-seq data? HOT 2
- Feature request HOT 7
- Low confidence result for all HLA genes HOT 10
- Question about minimap2 parameters in long_read_typing.py HOT 15
- complaining about dependencies / empty output files HOT 9
- what's the meanning of "interval_dict" in long_read_typing.py ? HOT 7
- how to get hla_gen.format.filter.extend.DRB.no26789.fasta ? HOT 5
- Couldn't run a test on example files of exon. I saw this error related to libtinfo.so.5: version `NCURSES_TINFO_5.0.19991023' HOT 6
- Typing long reads HOT 7
- Index command fails but reports success HOT 1
- how to assign read to gene ? HOT 1
- use deep-variants calling too to replace longshot ? HOT 1
- Reason for setting bias value for annoHLA.pl
- Bug report : Cannot find sample.realign.sort.bam for long read typing
- Got different allele result for different IMGT version
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 spechla.