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4
votes
0
answers
89
views
0
answers
Why difference in Hisat2 and bamqc from qualimap results?
bamqc qualimap rna-seq hisat2 written 6 days ago by Bioinfo • 170 • updated 5 days ago by Biostar ♦♦ 20
1
vote
2
answers
116
views
2
answers
Computer requirements for RNAseq alignment
rnaseq computer alignment hisat2 written 10 days ago by n.lu • 30 • updated 10 days ago by genomax ♦ 46k
2
votes
1
answer
71
views
1
answer
Alignment and Counting strandedness redundancy?
alignment featurecounts rna-seq strand hisat2 written 17 days ago by brismiller • 10 • updated 17 days ago by h.mon ♦ 13k
2
votes
0
answers
113
views
0
answers
Low read mapping efficiency with HISAT2
rna-seq hisat2 written 4 weeks ago by givans • 0 • updated 4 weeks ago by h.mon ♦ 13k
0
votes
0
answers
88
views
0
answers
What measure should be used to calculate fold-change while using Ballgown to compare D.E genes between 2 conditions?
ballgown stringtie rna-seq hisat2 written 4 weeks ago by nancy • 30
2
votes
2
answers
281
views
2
answers
Where to get >200Gb to build Bovine genome index in HISAT2?
genome indexing next-gen rna-seq hisat2 written 6 weeks ago by Hernán • 110
0
votes
0
answers
86
views
0
answers
RNA-seq read alignment to ref. genome-mismatch penalty
rna-seq hisat2 written 8 weeks ago by amy16 • 20
0
votes
0
answers
312
views
0
answers
Creating Hisat2 Index
genome hisat2 rna-seq index written 10 weeks ago by Bioinfo • 170
8
votes
2
answers
430
views
2
answers
Which strand specific option need to be used with HISAT2?
hisat2 rna-seq strandspecific written 10 weeks ago by Bioinfo • 170 • updated 10 weeks ago by JJ • 170
1
vote
0
answers
177
views
0
answers
Example data to verify of RNA-Seq Analysis pipeline
tutorial pipeline rna-seq hisat2 written 11 weeks ago by hkarakurt • 10
1
vote
1
answer
172
views
1
answer
Cufflinks gives only CUFF names with a gtf.
cufflinks rna-seq hisat2 written 12 weeks ago by hkarakurt • 10 • updated 12 weeks ago by Macspider • 2.3k
0
votes
1
answer
191
views
1
answer
HISAT2 running pair end
rna-seq hisat2 written 3 months ago by catagui • 20
2
votes
2
answers
246
views
2
answers
Hisat2 multiple paired end reads
allignment rna-seq hisat2 written 3 months ago by sicat.paolo20 • 0 • updated 3 months ago by Vijay Lakhujani • 1.9k
3
votes
1
answer
314
views
1
answer
Why different rna-seq aligners need to be used for Ion Torrent data compared with illumina?
tophat bbmap mira rna-seq hisat2 written 3 months ago by Bioinfo • 170 • updated 3 months ago by h.mon ♦ 13k
0
votes
1
answer
242
views
1
answer
Is there a way to separate highly similar strains from metatranscriptomic data using HISAT2?
metatranscriptomics rna-seq hisat2 written 3 months ago by sheinsch • 0 • updated 3 months ago by colindaven • 600
3
votes
1
answer
412
views
1
answer
What is the difference between HISAT2 index "genome.tran" and "genome"
hisat2 rna-seq index written 4 months ago by xchnju • 10 • updated 4 months ago by WouterDeCoster ♦ 27k
0
votes
0
answers
387
views
0
answers
hisat2-build indexing produces more than 8 output files
indexing hisat2 written 4 months ago by ddowlin • 50
0
votes
0
answers
292
views
0
answers
Alignment parameters within Hisat2
alignment rna-seq hisat2 written 5 months ago by amy16 • 20 • updated 4 months ago by Biostar ♦♦ 20
1
vote
1
answer
308
views
1
answer
Passing VCF file directly into ```HiSAT2-build --snp --haplotype```
next-gen alignment snp hisat2 written 4 months ago by rightmirem • 40
7
votes
2
answers
860
views
6 follow
2
answers
[RNAseq] Do anyone have already-built Hisat2 indexes files for human genome (GRCh37 ) ?
hisat2 indexes files rna-seq transcriptome written 10 months ago by atonidas • 0 • updated 4 months ago by ag1805x • 80
2
votes
1
answer
447
views
1
answer
HISAT2 indexes, GRCm38 or mm10?
hisat2 rna-seq index written 4 months ago by Buffo • 1.1k • updated 4 months ago by Sej Modha • 2.8k
5
votes
2
answers
430
views
2
answers
HISAT2 index creation
hisat2 rna-seq splice site index written 5 months ago by devbt15 • 10
2
votes
1
answer
371
views
1
answer
Misamtch penalty in RNA-seq alignment
rna-seq hisat2 written 5 months ago by amy16 • 20 • updated 5 months ago by Istvan Albert ♦♦ 76k
6
votes
2
answers
401
views
2
answers
RNA-seq read alignment
tophat hisat2 written 5 months ago by amy16 • 20
5
votes
1
answer
323
views
1
answer
HISAT2-2.0.1 is not installed
hisat2 written 5 months ago by XBria • 40 • updated 5 months ago by Sej Modha • 2.8k
0
votes
0
answers
317
views
0
answers
Downloading HISAT2-2.0.1 NOT possible
hisat2 written 5 months ago by XBria • 40
2
votes
1
answer
434
views
1
answer
Whether to use all aligned reads (QC-passed) or only properly-paired reads from rnaseq data?
ngs samtools properly-paired rna-seq hisat2 written 6 months ago by bioinfo8 • 90
64
votes
9
answers
2.9k
views
28 follow
9
answers
Forum: Stranger Things: unexpected limitations of popular tools
forum samtools errors hisat2 written 9 months ago by Istvan Albert ♦♦ 76k • updated 6 months ago by Charles Plessy • 2.4k
4
votes
1
answer
433
views
1
answer
Error while running rnaseq_pipeline.sh provided by hisat2
paired-end hisat2 rna-seq shell bash written 6 months ago by bioinfo8 • 90
6
votes
1
answer
735
views
5 follow
1
answer
How many index files will be generated from hisat2-build
hisat2 rna-seq index written 10 months ago by Xiaokang ZH • 30 • updated 6 months ago by sxm891114 • 0
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