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Showing : hisat2 • reset
4
Votes
3
Replies
138
Views
Extracting uniquely mapped reads from bams
rna-seq hisat2
20 months ago
gokberk • 30
0
Votes
0
Replies
111
Views
HiSAT2 edit distance option
rna-seq hisat2
20 months ago
gokberk • 30
0
Votes
11
Replies
197
Views
i want to convert .ht2 files into FASTA file
GATK FASTA HISAT2 Tool
20 months ago
saumya.sharma1509 • 0
0
Votes
5
Replies
168
Views
MarkDuplicates: Mates are missing
rna-seq trimmomatic Hisat2 picardtools samtools
20 months ago
swarajgaikwad15 • 0
2
Votes
9
Replies
3.7k
Views
Could not locate a HISAT2 index to basename
RNA-Seq Hisat2
3.6 years ago
oolongoni • 10 • updated 20 months ago
zhiminfdu • 0
0
Votes
1
Reply
236
Views
HISAT2 "error: Encountered internal HISAT2 exception (#1)"
hisat2 hisat
21 months ago
zhu.ge • 0
0
Votes
4
Replies
202
Views
Identify jumbled transcripts (scrambled exons) using HISAT2, stringtie, and GFFcompare?
RNA-SEQ hisat2 stringtie gffcompare
21 months ago
wolfgang.rumpf • 10 • updated 21 months ago
danbileedg2019 • 0
2
Votes
3
Replies
377
Views
Infer experiment - Failed to determine strandin paired end stranded RNA-seq
RNA-Seq HISAT2 STAR paired end stranded
2.1 years ago
GiusiG • 0 • updated 21 months ago
zoegward • 60
0
Votes
6
Replies
259
Views
Directional Strand related settings for RNA-seq Analysis Software
RNA-Seq HiSat2 Smartseq Tophat HTseq
21 months ago
BM • 40 • updated 21 months ago
Juke-34 ♦ 2.2k
0
Votes
0
Replies
264
Views
hisat2-stringtie-ballgown pipeline gives high p-value and q-value for RNA-seq of Arabidopsis thaliana
RNA-Seq hisat2 ballgown stringtie arabidopsis
22 months ago
tiancaigg • 0
1
Vote
1
Reply
311
Views
What dose this error of hisat2 mean? - (ERR): hisat2-align died with signal 11 (SEGV)
rna-seq HISAT2 mapping
22 months ago
tyaoi2 • 10 • updated 22 months ago
genomax 68k
0
Votes
1
Reply
165
Views
Read counts at specific locations in SAM files
RNA-Seq SAM hisat2
22 months ago
fogarty.mc • 0
2
Votes
5
Replies
276
Views
need help with script for hisat2 alignment
hisat2 alignment RNA-Seq
23 months ago
Antonio.Aubry • 10
5
Votes
6
Replies
326
Views
Problem in indexing toplevel genome with HISAT2
RNA-Seq genome hisat2 hisat2-build index
23 months ago
Batu • 150
2
Votes
6
Replies
332
Views
Why my Hisat2 result is 0% aligned concordantly and HTseq result is 100% not aligned.
RNA-Seq alignment Hisat2 HTseq
23 months ago
guotingfeng • 10 • updated 23 months ago
genomax 68k
1
Vote
1
Reply
335
Views
Can HISAT2 be invoked in bash shell, and can it be fed variables or names with wildcards as inputs?
HISAT2 Bash Shell batch jobs wild cards
23 months ago
RNAseqer • 110 • updated 23 months ago
RamRS 21k
3
Votes
8
Replies
246
Views
Selecting methods for performing pairwise RNAseq analysis without replicates
rna-seq DESeq2 DESeq Hisat2 tissues
23 months ago
bioinforesearchquestions • 230 • updated 23 months ago
i.sudbery 4.7k
0
Votes
4
Replies
284
Views
Hisat2 -Can it align paired readfiles, and unpaired read files leftover from trimming/QC simultaneously?
rna-seq alignment HISAT2 Paired end
23 months ago
RNAseqer • 110 • updated 23 months ago
h.mon 25k
1
Vote
2
Replies
264
Views
Reference sequence for indica Rice Paired End reads assembly using HISAT2
Referance Rice indica Assembly HISAT2
23 months ago
sharadlko1 • 0
0
Votes
1
Reply
464
Views
Hisat2 after the use of trimmomatic software: (ERR): hisat2-align exited with value 134
trimmomatic RNA-Seq Hisat2 new tuxedo protocol
24 months ago
swarajgaikwad15 • 0 • updated 24 months ago
ATpoint 17k
4
Votes
3
Replies
288
Views
Strange output of samtools flag stat?
RNA-Seq samtools HISAT2 mouse
24 months ago
heking • 0 • updated 24 months ago
Istvan Albert 87k
4
Votes
8
Replies
427
Views
Stringtie elimination of important transcripts
RNA-Seq alignment assembly stringtie hisat2
2.0 years ago
ra2967 • 10
0
Votes
2
Replies
493
Views
How to map RNA-seq with hisat2, stringtie, an assembly fasta, a gtf file, and a transcript fasta?
hisat2 mapping transcriptome stringtie
2.0 years ago
O.rka • 110 • updated 2.0 years ago
swbarnes2 5.7k
3
Votes
12
Replies
354
Views
6 follow
RNA-Seq Differential Expression Bash Scripting Error
RNA-Seq pipeline bash scripting hisat2 samtools
2.0 years ago
timothyfisher101 • 0 • updated 2.0 years ago
ATpoint 17k
2
Votes
6
Replies
393
Views
How to identify RNA-seq mapped reads to reference genome but not identified by featurecounts of Subread package?
RNA-Seq featureCounts HISAT2
2.1 years ago
bk11 • 30 • updated 2.1 years ago
kristoffer.vittingseerup ♦ 1.8k
1
Vote
2
Replies
232
Views
How to handle RNASeq reads that can map to both human and mouse ref (e.g. conserved gene regions)?
alignment hisat2
2.1 years ago
DVA • 520 • updated 2.1 years ago
JC 7.9k
0
Votes
1
Reply
402
Views
Hisat2 output for stringtie
hisat2 stringtie
2.2 years ago
Sam • 110 • updated 2.2 years ago
Vijay Lakhujani 4.1k
3
Votes
5
Replies
398
Views
how to extract counts from bam/merge-bam without gtf
RNA-Seq R bowtie2 samtools Hisat2
2.2 years ago
Shahzad • 10 • updated 2.2 years ago
michael.ante ♦ 3.3k
0
Votes
3
Replies
764
Views
hisat2 and RSEM pipeline
rna-seq software error hisat2 gtf RSEM
2.2 years ago
Shahzad • 10 • updated 2.2 years ago
EagleEye 6.4k
2
Votes
3
Replies
466
Views
Sorting BAM files from HISAT2 for DEXSeq
RNA-Seq hisat2 dexseq
2.2 years ago
squando • 10 • updated 2.2 years ago
Ian 5.4k
1
Vote
2
Replies
391
Views
HISAT2 SRR error
rna-seq alignment SRA SRR HISAT2
2.2 years ago
NAVID.BAVI • 0 • updated 2.2 years ago
genomax 68k
5
Votes
14
Replies
861
Views
HISAT2 Indexing using annotation for Rattus_norvegicus
HISAT2 annotation Ensembl index alignment
2.2 years ago
neranjan • 20
1
Vote
1
Reply
506
Views
Is HISAT2 able to output only the best alignment?
HISAT2
2.4 years ago
RoseString • 10 • updated 2.2 years ago
prasundutta87 • 330
3
Votes
14
Replies
762
Views
best pipeline to get gene and transcript counts
RNA-Seq alignment count Hisat2 STAR
2.2 years ago
lkianmehr • 30 • updated 2.2 years ago
t.blasco95 • 30
1
Vote
5
Replies
289
Views
To fetch the reads which are being partially mapped to the genome
RNA-Seq Bowtie2 HISAT2 STAR jvarkit
2.3 years ago
swadha • 20 • updated 2.3 years ago
genomax 68k
0
Votes
9
Replies
451
Views
Is TCGA Breast cancer data strand specific?
RNA-Seq tcga strand geneexpression hisat2
2.3 years ago
Vasu • 330 • updated 2.3 years ago
genomax 68k
1
Vote
3
Replies
257
Views
Hisat2 alignment results can be ued for TEtoolkit analysis
Hisat2 TEtoolkit
2.3 years ago
lkianmehr • 30 • updated 2.3 years ago
h.mon 25k
5
Votes
5
Replies
414
Views
Ovation RNA-seq system, bionfomatic alignment and htseq-count
RNA-Seq hisat2 htseq-count
2.3 years ago
nanoide • 30 • updated 2.3 years ago
caggtaagtat • 620
2
Votes
2
Replies
276
Views
Why chromosome coordinates were given for unmapped reads in hisat2?
hisat2 RNA-seq Unmapped alignment
2.3 years ago
xieshaojun0621 • 120
2
Votes
1
Reply
490
Views
HISAT2-build killed: 9 macOS
RNA-Seq hisat2 build index
2.3 years ago
datascientist28 • 390
2
Votes
14
Replies
442
Views
fastq file do not look as they should (running Hisat2)
hisat2 RNA-Seq fastq
2.3 years ago
luzglongoria • 20
6
Votes
6
Replies
593
Views
Compatibility between my reference genome and GTF file
rna-seq hisat2 alignment reference genome
2.3 years ago
Batu • 150
5
Votes
8
Replies
469
Views
How to bring consistency for genome reference, annotation and index files?
RNA-Seq hisat2 genome gencode annotation
2.3 years ago
Vasu • 330
8
Votes
12
Replies
613
Views
hisat2 warning message dunring alignment of fasta file with reference genome
RNA-Seq software error next-gen alignment hisat2
2.3 years ago
shuksi1984 • 50 • updated 2.3 years ago
singh.vijender • 30
2
Votes
1
Reply
345
Views
How to deal with single transcripts assigned to multiple genes?
RNA-Seq StringTie hisat2
2.3 years ago
antoinefelden • 20 • updated 2.3 years ago
RamRS 21k
2
Votes
9
Replies
894
Views
hisat2 / bowtie: read has more quality values than read characters
bowtie2 hisat2 hisat bowtie
2.3 years ago
juan.crescente • 20
2
Votes
7
Replies
426
Views
Proper design for DESeq2 and other RNAseq general questions
RNA-Seq DESeq2 Hisat2 Stringtie
2.3 years ago
Stef • 0 • updated 2.3 years ago
swbarnes2 5.7k
6
Votes
7
Replies
530
Views
Problem mapping with STAR
STAR TopHat HISAT2
2.4 years ago
alvarocentron91 • 10 • updated 2.4 years ago
WouterDeCoster 39k
1
Vote
2
Replies
400
Views
Prepare multiple gtf files for Ballgown
RNA-Seq hisat2 hisat
2.4 years ago
catglen012 • 0
0
Votes
0
Replies
418
Views
Advantage of making HISAT2 genome index with annotation file
hisat2 reference index annotations
2.4 years ago
piyushjo • 110 • updated 2.4 years ago
RamRS 21k
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