Skip to content

Issues: DaehwanKimLab/hisat2

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

217 Open 144 Closed
217 Open 144 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

(ERR): Expected hisat2 to be in same directory with hisat2-align-s and hisat2-align-l:
#446 opened Dec 11, 2024 by mcastilloli2
--sra-acc argument behavior
#444 opened Nov 13, 2024 by el239
Should I run hisat2 in a 2-pass mode for better mapping at novel junctions?
#443 opened Nov 9, 2024 by weishwu
Build index with hisat-3n, but one of the generated ht2 files is empty
#441 opened Sep 19, 2024 by yaoyf03
1
Samtools format errors
#440 opened Sep 2, 2024 by paulinarosales
Enabling a --temp-directory parameter
#438 opened Aug 6, 2024 by pasviber
3
Support Third-generation full-length RNA-seq?
#437 opened Jul 29, 2024 by yjiang296
Question about Hisat-3N align
#436 opened Jul 24, 2024 by bugandong
Question about calculation of base counts in hisat3Ntable
#433 opened Jun 21, 2024 by shen-lanlan
--directional-mapping-reverse vs. --rna-strandness on HISAT3N
#432 opened Jun 17, 2024 by paulinarosales
(ERR): "ref.genome" does not exist Exiting now ...
#431 opened Jun 8, 2024 by Anees-caas
Mapping using different parameters --very-sensitive and default
#430 opened May 14, 2024 by AllanOkwaro
Issue with hisatgenotype
#429 opened Apr 13, 2024 by Januaryyiyue
2
[Future request] hisat-3n table option to report conversions summarized to genomic feature or reads counts
#428 opened Apr 4, 2024 by paulinarosales
hisat2-build failed for Segmentation fault
#427 opened Apr 1, 2024 by yqlan
hisat2-build index for circRNA-seq
#426 opened Mar 27, 2024 by fengweimin-maker
Hisat-3N mapping quality
#425 opened Mar 7, 2024 by ZiggeyQi
hisat2 location does not exist
#424 opened Feb 20, 2024 by Thanatia
[Bug Report] hisat2-align exited with value 137, space complexity of hisat2
#423 opened Dec 11, 2023 by bayegy
ERR): "fastq file.fastq" does not exist. Exiting now ...
#422 opened Nov 24, 2023 by big-boo1
-np argument seemingly not working
#421 opened Nov 9, 2023 by brian-odonovan
Any plans to support Apple Silicon architecture?
#419 opened Sep 30, 2023 by itslittman
1
Please add the pbat option of hisat-3n
#416 opened Jul 23, 2023 by kekaiko
Output files(.snp, .haplotype) of hisat2_extract_snps_haplotypes_*.py are empty
#414 opened Jul 13, 2023 by jim83830
Feature request: Add support for xz and zstd
#412 opened Jun 22, 2023 by outpaddling
ProTip! Type g i on any issue or pull request to go back to the issue listing page.