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217 Open 144 Closed
217 Open 144 Closed
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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
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