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3
votes
1
answer
64
views
1
answer
Remove secondary alignments in RNA-seq analysis?
alignment rna-seq hisat2 written 2 days ago by nanoide • 10
2
votes
0
answers
182
views
0
answers
What is the prefered script for HISAT2 genome-guided using draft genome? --dta or --exon ?
genome guided alignment rna-seq hisat2 written 16 days ago by Farbod • 3.1k
3
votes
0
answers
138
views
0
answers
HISAT2 relaxing parameters?
mismatches alignment mapping rna-seq hisat2 written 13 days ago by biogirl04 • 0
0
votes
0
answers
108
views
0
answers
hisat2 --sra-acc with paired reads producing single read output
sra-tools hisat2 written 7 weeks ago by avp25 • 0 • updated 16 days ago by Biostar ♦♦ 20
1
vote
1
answer
101
views
1
answer
Adding tag XS to HISAT2 sam files perior to StringTie
stringtie alignment samtools rna-seq hisat2 written 20 days ago by Farbod • 3.1k • updated 20 days ago by Vijay Lakhujani ♦ 2.8k
7
votes
1
answer
142
views
1
answer
Mapping paired-end reads to a draft genome using HISAT2
genome guided alignment rna-seq hisat2 written 25 days ago by Farbod • 3.1k • updated 25 days ago by genomax ♦ 51k
2
votes
0
answers
238
views
0
answers
Hisat2 index building taking days even with 40 GB RAM
sequencing build hisat2 written 11 weeks ago by piyushjo • 0 • updated 4 weeks ago by Biostar ♦♦ 20
1
vote
0
answers
231
views
0
answers
Why I see very high mapping percentage, Is this normal or anything wrong in generating libraries?
samtools mapping rna-seq hisat2 written 12 weeks ago by Bioinfo • 220 • updated 7 weeks ago by Biostar ♦♦ 20
1
vote
1
answer
162
views
1
answer
stringtie merged gtf doesn't give any gene expression columns
stringtie merge rna-seq hisat2 written 8 weeks ago by Biologist • 60 • updated 8 weeks ago by Kevin Blighe ♦ 24k
0
votes
0
answers
101
views
0
answers
Use normalised reads for HISAT2/Braker1
gene prediction braker normalisation hisat2 written 8 weeks ago by ersgupta • 0
4
votes
1
answer
679
views
6 follow
1
answer
What is the difference between HISAT2 index "genome.tran" and "genome"
hisat2 rna-seq index written 6 months ago by xchnju • 20 • updated 10 weeks ago by li.anlin666 • 0
2
votes
2
answers
247
views
5 follow
2
answers
Evaluation of HISAT2 Alignment Result
alignment rna-seq hisat2 written 10 weeks ago by modarzi • 20 • updated 10 weeks ago by Vijay Lakhujani ♦ 2.8k
0
votes
0
answers
132
views
0
answers
Primary assembly or patches: what to choose for making index file?
genome hisat2 index written 11 weeks ago by piyushjo • 0
0
votes
1
answer
177
views
1
answer
HISAT2-StringTie-CuffDiff "Sam file doesn't appear to be correctly sorted"
stringtie cuffdiff rna-seq hisat2 written 11 weeks ago by aboyher • 0 • updated 11 weeks ago by JJ • 320
4
votes
0
answers
210
views
0
answers
Why difference in Hisat2 and bamqc from qualimap results?
bamqc qualimap rna-seq hisat2 written 3 months ago by Bioinfo • 220 • updated 3 months ago by Biostar ♦♦ 20
1
vote
2
answers
325
views
2
answers
Computer requirements for RNAseq alignment
rnaseq computer alignment hisat2 written 3 months ago by n.lu • 30 • updated 3 months ago by genomax ♦ 51k
2
votes
1
answer
162
views
1
answer
Alignment and Counting strandedness redundancy?
alignment featurecounts rna-seq strand hisat2 written 3 months ago by brismiller • 10 • updated 3 months ago by h.mon ♦ 16k
2
votes
0
answers
221
views
0
answers
Low read mapping efficiency with HISAT2
rna-seq hisat2 written 4 months ago by givans • 0 • updated 4 months ago by h.mon ♦ 16k
0
votes
0
answers
201
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 months ago by nancy • 60
2
votes
2
answers
384
views
2
answers
Where to get >200Gb to build Bovine genome index in HISAT2?
genome indexing next-gen rna-seq hisat2 written 4 months ago by Hernán • 110
0
votes
0
answers
112
views
0
answers
RNA-seq read alignment to ref. genome-mismatch penalty
rna-seq hisat2 written 4 months ago by amy16 • 20
0
votes
0
answers
602
views
0
answers
Creating Hisat2 Index
genome hisat2 rna-seq index written 5 months ago by Bioinfo • 220
11
votes
2
answers
785
views
7 follow
2
answers
Which strand specific option need to be used with HISAT2?
hisat2 rna-seq strandspecific written 5 months ago by Bioinfo • 220 • updated 5 months ago by JJ • 320
1
vote
0
answers
287
views
0
answers
Example data to verify of RNA-Seq Analysis pipeline
tutorial pipeline rna-seq hisat2 written 5 months ago by hkarakurt • 20
2
votes
1
answer
301
views
1
answer
Cufflinks gives only CUFF names with a gtf.
cufflinks rna-seq hisat2 written 5 months ago by hkarakurt • 20 • updated 5 months ago by Macspider • 2.4k
0
votes
1
answer
269
views
1
answer
HISAT2 running pair end
rna-seq hisat2 written 6 months ago by catagui • 20
5
votes
2
answers
392
views
2
answers
Hisat2 multiple paired end reads
allignment rna-seq hisat2 written 6 months ago by sicat.paolo20 • 20 • updated 6 months ago by Vijay Lakhujani ♦ 2.8k
3
votes
1
answer
457
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 6 months ago by Bioinfo • 220 • updated 6 months ago by h.mon ♦ 16k
0
votes
1
answer
296
views
1
answer
Is there a way to separate highly similar strains from metatranscriptomic data using HISAT2?
metatranscriptomics rna-seq hisat2 written 6 months ago by sheinsch • 0 • updated 6 months ago by colindaven • 730
0
votes
0
answers
556
views
0
answers
hisat2-build indexing produces more than 8 output files
indexing hisat2 written 7 months ago by ddowlin • 50
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