Comments (10)
It would be extremely nice if Hisat2 produced "split" reads (besides discordants) so that we could replace STAR in Manta fusion calling for hg38.
from hisat2.
I'm wondering if this ever made progresss
from hisat2.
Yes, I plan to implement in HISAT2 fusion alignment and reporting fusions that are strongly supported by reads, similar to TopHat-Fusion. HISAT2's fusion detection will be much faster and more sensible than TopHat-Fusion. Hopefully I will release a working version by spring of next year.
from hisat2.
Excellent.
from hisat2.
Are there any advances in the implement of HISAT2 fusion alignment? Thanks!
from hisat2.
I would also be interested in this!
from hisat2.
@infphilo could we please reopen this issue? I believe there is sufficient interest for fusion calling and it would really be a great addition to Hisat2. @mjafin, are you guys doing RNA-Seq fusion calling on hg38?
from hisat2.
I reopened this feature request. I know we need a fast and more accurate fusion finding program, and HISAT2 could be a good starting point.
Implementing a fusion calling algorithm may take at least several months (or even more). I won't be able to implement it myself. I'm looking to have my own lab and work with students or postdocs to develop a new method.
from hisat2.
We're also very interested in developing HISAT-fusion, but we have our hands full with many projects now. Perhaps, one way to help us out is to encourage potential postdocs with strong computational skills to apply for our lab, kim-lab.org.
from hisat2.
We're also very interested in developing HISAT-fusion, but we have our hands full with many projects now. Perhaps, one way to help us out is to encourage potential postdocs with strong computational skills to apply for our lab, kim-lab.org.
Can anyone write here about Hisat2-fusion?
from hisat2.
Related Issues (20)
- Question regarding the runtime for hisat-3n-table
- hisat2-build DOES NOT work for me! HOT 1
- building standard hisat-3n indices with --base-change but not --repeat-index HOT 4
- "Local Graph Exploded" warning for hisat2 build using --snp,--haplotype,--exon and --ss.
- Hisat2 [Errno 2] No such file or directory
- Align ATAC-seq with Hisat2?
- error minimum intron length with hisat2 v. 2.2.1
- Repeat mapping with different result
- Feature request: Add support for xz and zstd
- hisat2 hangs aligning axolotl reads HOT 1
- Output files(.snp, .haplotype) of hisat2_extract_snps_haplotypes_*.py are empty
- Please add the pbat option of hisat-3n
- A question about methylation information extraction
- Any plans to support Apple Silicon architecture?
- Installation Issue Error 1 - make HOT 1
- -np argument seemingly not working
- ERR): "fastq file.fastq" does not exist. Exiting now ...
- [Bug Report] hisat2-align exited with value 137, space complexity of hisat2
- hisat2 location does not exist
- Hisat-3N mapping quality
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from hisat2.