DaehwanKimLab hisat2 issues

DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)

GNU General Public License v3.0

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issues

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Remove the imp dependency in hisat2-inspect

#445 mourisl closed 1 week ago
0
--sra-acc argument behavior

#444 el239 opened 1 week ago
0
Should I run hisat2 in a 2-pass mode for better mapping at novel junctions?

#443 weishwu opened 1 week ago
0
Properly handle the option temp-directory through the wrapper

#442 mourisl closed 1 week ago
0
Build index with hisat-3n, but one of the generated ht2 files is empty

#441 yaoyf03 opened 2 months ago
1
Samtools format errors

#440 paulinarosales opened 2 months ago
0
fix hisat2 performance: remove unused SpliceSiteDB from AlnSink

#439 yttria-aniseia closed 3 months ago
1
Enabling a --temp-directory parameter

#438 pasviber opened 3 months ago
3
Support Third-generation full-length RNA-seq?

#437 yjiang296 opened 3 months ago
0
Question about Hisat-3N align

#436 bugandong opened 4 months ago
0
Add Python3.12 support by removing use of the "imp" module

#435 mr-c closed 1 week ago
1
mkfifo failed error and change $temp_dir

#434 pxchen110 closed 4 months ago
1
Question about calculation of base counts in hisat3Ntable

#433 shen-lanlan opened 5 months ago
0
--directional-mapping-reverse vs. --rna-strandness on HISAT3N

#432 paulinarosales opened 5 months ago
0
(ERR): "ref.genome" does not exist Exiting now ...

#431 Anees-caas opened 5 months ago
0
Mapping using different parameters --very-sensitive and default

#430 AllanOkwaro opened 6 months ago
0
Issue with hisatgenotype

#429 Januaryyiyue opened 7 months ago
2
[Future request] hisat-3n table option to report conversions summarized to genomic feature or reads counts

#428 paulinarosales opened 7 months ago
0
hisat2-build failed for Segmentation fault

#427 yqlan opened 7 months ago
0
hisat2-build index for circRNA-seq

#426 fengweimin-maker opened 8 months ago
0
Hisat-3N mapping quality

#425 ZiggeyQi opened 8 months ago
0
hisat2 location does not exist

#424 Thanatia opened 9 months ago
0
[Bug Report] hisat2-align exited with value 137, space complexity of hisat2

#423 bayegy opened 11 months ago
0
ERR): "fastq file.fastq" does not exist. Exiting now ...

#422 big-boo1 opened 12 months ago
0
-np argument seemingly not working

#421 brian-odonovan opened 1 year ago
0
Installation Issue Error 1 - make

#420 ntorres17 closed 1 year ago
2
Any plans to support Apple Silicon architecture?

#419 itslittman opened 1 year ago
1
adding script to index latest human telomere-to-telomere genome provided at NCBI

#418 animesh opened 1 year ago
0
A question about methylation information extraction

#417 kekaiko closed 1 year ago
0
Please add the pbat option of hisat-3n

#416 kekaiko opened 1 year ago
0
add native support for gzipped fastq files

#415 CJ-Chen closed 1 year ago
1
Output files(.snp, .haplotype) of hisat2_extract_snps_haplotypes_*.py are empty

#414 jim83830 opened 1 year ago
0
hisat2 hangs aligning axolotl reads

#413 outpaddling closed 1 year ago
1
Feature request: Add support for xz and zstd

#412 outpaddling opened 1 year ago
0
Repeat mapping with different result

#411 BioLaoXu opened 1 year ago
0
error minimum intron length with hisat2 v. 2.2.1

#410 ConcettaDe4 opened 1 year ago
0
Align ATAC-seq with Hisat2?

#409 yjiang296 opened 1 year ago
0
Add CI for Linux aarch64

#408 martin-g opened 1 year ago
0
Add Github Actions based CI for Linux x86_64

#407 martin-g opened 1 year ago
3
Make hisat2 compilable with Visual Studio 2019

#406 teepean opened 1 year ago
0
Hisat2 [Errno 2] No such file or directory

#405 mmtohm closed 1 year ago
0
"Local Graph Exploded" warning for hisat2 build using --snp,--haplotype,--exon and --ss.

#404 SJJHK opened 1 year ago
0
building standard hisat-3n indices with --base-change but not --repeat-index

#403 connertraugot closed 1 year ago
4
hisat2-build DOES NOT work for me!

#402 zerolinuxbio opened 1 year ago
1
Question regarding the runtime for hisat-3n-table

#401 cahn20 opened 1 year ago
0
mapped read length

#400 wangjiawen2013 opened 1 year ago
0
*** Error in `hisat2-build': double free or corruption (!prev): 0x00002b5724374370 ***

#399 rvarki closed 1 year ago
1
Forcing alignment only to the forward reference for HISAT-3N

#398 cahn20 opened 1 year ago
1
Could not locate a HISAT2 index

#397 hasanalanya closed 1 year ago
2
(ERR): hisat2-align died with signal 6 (ABRT) (core dumped)

#396 dianzhiyong opened 2 years ago
3