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3
votes
1
answer
194
views
1
answer
hisat2 parameters for paired end and single end reads from same samples
hisat stringtie alignment rna-seq hisat2 written 10 days ago by bioinfo17 • 10 • updated 9 days ago by Macspider • 1.5k
0
votes
0
answers
118
views
0
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Set percent identity and percent length covered in HISAT2 mapping
read hisat2 mapping genomics sequencing written 9 days ago by O.rka • 30
13
votes
2
answers
294
views
6 follow
2
answers
Too low mapping percentage using HISAT2 on human reference genome.
genome cell line hisat2 written 18 days ago by Vijay Lakhujani • 1.2k
2
votes
1
answer
212
views
1
answer
hisat2 run gave 0% alignment
alignment rna-seq hisat2 written 5 weeks ago by vinayjrao • 60 • updated 5 weeks ago by Satyajeet Khare • 1.0k
5
votes
2
answers
3.5k
views
2
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Hisat R strandness aligning same strand as F strandness, how to do it correctly?
hisat2 alignment strandness rna-seq ribo-zero written 14 months ago by Niek De Klein • 2.4k • updated 8 weeks ago by agolicz • 10
1
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0
answers
301
views
0
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Error HISAT2 output for HTseq-count
htseq-count rna-seq hisat2 written 9 weeks ago by nicolas.merienne • 0
45
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6
answers
1.7k
views
25 follow
6
answers
Forum: Stranger Things: unexpected limitations of popular tools
forum samtools errors hisat2 written 10 weeks ago by Istvan Albert ♦♦ 73k • updated 9 weeks ago by dariober • 8.0k
0
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3
answers
256
views
3
answers
Mapping onto the Transcriptome, RNA-seq
transcriptome rna-seq bowtie hisat2 written 10 weeks ago by asyndeton17 • 10 • updated 10 weeks ago by Rob ♦ 2.1k
2
votes
2
answers
370
views
2
answers
HISAT2 rna-strandness option
rna-seq hisat2 written 10 weeks ago by cpak1981 • 30 • updated 10 weeks ago by Antonio R. Franco • 3.4k
4
votes
0
answers
1.7k
views
0
answers
Hisat2 versus Bowtie2
bowtie2 exome-sequencing hisat2 written 16 months ago by nalpas.nicolas • 20 • updated 10 weeks ago by Biostar ♦♦ 20
2
votes
1
answer
225
views
1
answer
HISAT2: does the parameter -k 1 means unique mapping?
hisat2 written 11 weeks ago by biolab • 950 • updated 11 weeks ago by WouterDeCoster ♦ 21k
1
vote
0
answers
186
views
0
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Is it necessary to include --known-splicesite-infile in HISAT2?
hisat2 written 11 weeks ago by biolab • 950
0
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0
answers
208
views
0
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Hisat2 warning: skipping mate
tophat2 ngs alignment hisat2 written 12 weeks ago by veronicaschroeder78 • 100
6
votes
1
answer
257
views
1
answer
How many index files will be generated from hisat2-build
hisat2 rna-seq index written 3 months ago by Xiaokang ZH • 20 • updated 3 months ago by Devon Ryan ♦ 70k
8
votes
1
answer
370
views
5 follow
1
answer
hisat2 parameters tuning to match tophat2 parameters
parameters tophat2 rna-seq hisat2 written 3 months ago by pierre.ortalo • 0 • updated 3 months ago by Istvan Albert ♦♦ 73k
0
votes
1
answer
416
views
1
answer
Strand-option in hisat2
rna-seq strand hisat2 written 3 months ago by vm.higareda • 0
1
vote
2
answers
292
views
2
answers
Could not locate a HISAT2 index to basename
rna-seq hisat2 written 3 months ago by oolongoni • 0 • updated 3 months ago by Vijay Lakhujani • 1.2k
1
vote
0
answers
197
views
0
answers
HISAT2 new release --avoid-pseudogene
rna-seq hisat2 written 3 months ago by badribio • 200
6
votes
2
answers
286
views
2
answers
[RNAseq] Do anyone have already-built Hisat2 indexes files for human genome (GRCh37 ) ?
hisat2 indexes files rna-seq transcriptome written 3 months ago by atonidas • 0 • updated 3 months ago by vignesh • 90
6
votes
2
answers
312
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5 follow
2
answers
Mapping RNA-Seq data on genome from another species
genome hisat2 star rna-seq mapping written 4 months ago by tlorin • 170 • updated 4 months ago by Brian Bushnell ♦ 14k
0
votes
1
answer
312
views
1
answer
HISAT2 error running both --dta and --min and --max-intronlen
hisat rna-seq hisat2 written 4 months ago by GLFR • 0 • updated 4 months ago by Vijay Lakhujani • 1.2k
0
votes
0
answers
196
views
0
answers
hisat2 extract snps haplotypes VCF.py: AssertionError
snps hisat2 written 4 months ago by christian.cortes.campos • 0 • updated 4 months ago by WouterDeCoster ♦ 21k
0
votes
0
answers
332
views
0
answers
HISAT2 and Stringtie: difference in Stringtie results when using pre-built indexes or creating new ones in HISAT2
hisat2 written 4 months ago by iraun • 3.1k
2
votes
2
answers
621
views
2
answers
How to build Hisat2 index for human genome (GRCh37 )?
rna-seq hisat2 written 4 months ago by vignesh • 90 • updated 4 months ago by h.mon ♦ 8.7k
0
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0
answers
323
views
0
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HISAT2 not reporting all splice sites?
splicing rna-seq splice sites hisat2 written 4 months ago by kapoozy • 0
0
votes
0
answers
401
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0
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hisat2 lead to highly multimapping rate
alignment rna-seq hisat2 written 7 months ago by yuxinghai • 0
0
votes
0
answers
354
views
0
answers
Access to HISAT2 folder under miniconda
software error sequencing next-gen hisat2 written 8 months ago by wq • 0 • updated 8 months ago by Devon Ryan ♦ 70k
5
votes
1
answer
516
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1
answer
Differential expression analysis with RNA-Seq samples that vary in depth
cufflinks depth of sequencing rna-seq hisat2 written 8 months ago by Satyajeet Khare • 1.0k • updated 8 months ago by Devon Ryan ♦ 70k
1
vote
1
answer
563
views
1
answer
HISAT2 : Differences in paired and unpaired rates
assembly alignment hisat2 written 9 months ago by gwe3409 • 0 • updated 9 months ago by Devon Ryan ♦ 70k
1
vote
1
answer
642
views
1
answer
fastq.gz Error: Not in gzip format
rnaseq hisat2 written 9 months ago by V • 50 • updated 9 months ago by Chris Miller ♦ 18k
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