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8
votes
1
answer
123
views
6 follow
1
answer
hisat2 warning message dunring alignment of fasta file with reference genome
software error next-gen alignment rna-seq hisat2 written 9 hours ago by shuksi1984 • 30 • updated 1 hour ago by singh.vijender • 20
2
votes
1
answer
74
views
1
answer
How to deal with single transcripts assigned to multiple genes?
stringtie rna-seq hisat2 written 4 days ago by antoinefelden • 20 • updated 1 day ago by RamRS ♦ 17k
2
votes
1
answer
85
views
1
answer
hisat2 / bowtie: read has more quality values than read characters
bowtie2 hisat2 bowtie hisat written 6 days ago by juan.crescente • 20
0
votes
2
answers
94
views
5 follow
2
answers
Proper design for DESeq2 and other RNAseq general questions
stringtie deseq2 rna-seq hisat2 written 4 days ago by Stef • 0 • updated 4 days ago by swbarnes2 ♦ 4.0k
6
votes
1
answer
156
views
1
answer
Problem mapping with STAR
tophat star hisat2 written 11 days ago by alvarocentron91 • 0 • updated 11 days ago by WouterDeCoster ♦ 32k
1
vote
0
answers
116
views
0
answers
Prepare multiple gtf files for Ballgown
hisat rna-seq hisat2 written 13 days ago by catglen012 • 0
0
votes
0
answers
101
views
0
answers
Is HISAT2 able to output only the best alignment?
hisat2 written 13 days ago by RoseString • 0 • updated 13 days ago by RamRS ♦ 17k
0
votes
0
answers
84
views
0
answers
Advantage of making HISAT2 genome index with annotation file
reference index annotations hisat2 written 14 days ago by piyushjo • 40 • updated 13 days ago by RamRS ♦ 17k
8
votes
0
answers
9.7k
views
0
answers
The comparison between HISAT2 and Tophat2
tophat2 rna-seq hisat2 written 2.6 years ago by Peng Huang • 50 • updated 19 days ago by RamRS ♦ 17k
0
votes
0
answers
120
views
0
answers
add read group with hisat2
algnment read group hisat2 written 5 weeks ago by marongiu.luigi • 310
1
vote
0
answers
794
views
6 follow
0
answers
hisat2-build indexing produces more than 8 output files
indexing hisat2 written 9 months ago by ddowlin • 60 • updated 6 weeks ago by gaoyufeng1109 • 0
1
vote
0
answers
749
views
0
answers
Hisat2 warning: skipping mate
ngs alignment hisat2 written 15 months ago by veronicaschroeder78 • 100 • updated 8 weeks ago by ATpoint ♦ 7.5k
2
votes
1
answer
156
views
1
answer
Hisat2 multimapped reads
alignment rna-seq hisat2 written 8 weeks ago by corend • 50 • updated 8 weeks ago by Devon Ryan ♦ 84k
4
votes
0
answers
343
views
0
answers
hisat2 was not worked
dyld rna-seq hisat2 written 9 weeks ago by mikan03orange • 0
5
votes
1
answer
165
views
1
answer
Remove secondary alignments in RNA-seq analysis?
alignment rna-seq hisat2 written 9 weeks ago by nanoide • 10
2
votes
0
answers
304
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 11 weeks ago by Farbod • 3.1k
3
votes
0
answers
229
views
0
answers
HISAT2 relaxing parameters?
mismatches alignment mapping rna-seq hisat2 written 11 weeks ago by biogirl04 • 0
0
votes
0
answers
197
views
0
answers
hisat2 --sra-acc with paired reads producing single read output
sra-tools hisat2 written 3 months ago by avp25 • 0 • updated 11 weeks ago by Biostar ♦♦ 20
1
vote
1
answer
212
views
1
answer
Adding tag XS to HISAT2 sam files perior to StringTie
stringtie alignment samtools rna-seq hisat2 written 12 weeks ago by Farbod • 3.1k • updated 12 weeks ago by Vijay Lakhujani ♦ 3.0k
7
votes
1
answer
242
views
1
answer
Mapping paired-end reads to a draft genome using HISAT2
genome guided alignment rna-seq hisat2 written 3 months ago by Farbod • 3.1k • updated 3 months ago by genomax ♦ 55k
2
votes
0
answers
346
views
0
answers
Hisat2 index building taking days even with 40 GB RAM
sequencing build hisat2 written 5 months ago by piyushjo • 40 • updated 3 months ago by Biostar ♦♦ 20
1
vote
0
answers
279
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 5 months ago by Bioinfo • 240 • updated 3 months ago by Biostar ♦♦ 20
1
vote
1
answer
343
views
1
answer
stringtie merged gtf doesn't give any gene expression columns
stringtie merge rna-seq hisat2 written 4 months ago by Biologist • 70 • updated 4 months ago by Kevin Blighe ♦ 28k
0
votes
0
answers
144
views
0
answers
Use normalised reads for HISAT2/Braker1
gene prediction braker normalisation hisat2 written 4 months ago by ersgupta • 0
4
votes
1
answer
885
views
6 follow
1
answer
What is the difference between HISAT2 index "genome.tran" and "genome"
hisat2 rna-seq index written 9 months ago by xchnju • 20 • updated 4 months ago by li.anlin666 • 0
3
votes
2
answers
436
views
5 follow
2
answers
Evaluation of HISAT2 Alignment Result
alignment rna-seq hisat2 written 4 months ago by modarzi • 20 • updated 4 months ago by Vijay Lakhujani ♦ 3.0k
0
votes
0
answers
193
views
0
answers
Primary assembly or patches: what to choose for making index file?
genome hisat2 index written 4 months ago by piyushjo • 40
0
votes
1
answer
277
views
1
answer
HISAT2-StringTie-CuffDiff "Sam file doesn't appear to be correctly sorted"
stringtie cuffdiff rna-seq hisat2 written 4 months ago by aboyher • 0 • updated 4 months ago by JJ • 320
4
votes
0
answers
333
views
0
answers
Why difference in Hisat2 and bamqc from qualimap results?
bamqc qualimap rna-seq hisat2 written 5 months ago by Bioinfo • 240 • updated 5 months ago by Biostar ♦♦ 20
1
vote
2
answers
552
views
2
answers
Computer requirements for RNAseq alignment
rnaseq computer alignment hisat2 written 5 months ago by n.lu • 30 • updated 5 months ago by genomax ♦ 55k
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