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<prev • 111 results • page 1 of 4 • next >
2
votes
2
answers
93
views
2
answers
how to extract counts from bam/merge-bam without gtf
R samtools bowtie2 rna-seq hisat2 written 8 days ago by Shahzad • 10 • updated 8 days ago by michael.ante • 2.7k
0
votes
1
answer
79
views
1
answer
hisat2 and RSEM pipeline
software error gtf rna-seq rsem hisat2 written 10 days ago by Shahzad • 10 • updated 10 days ago by EagleEye ♦ 5.9k
2
votes
1
answer
147
views
1
answer
Sorting BAM files from HISAT2 for DEXSeq
dexseq rna-seq hisat2 written 15 days ago by squando • 10 • updated 15 days ago by Ian ♦ 5.3k
1
vote
0
answers
102
views
0
answers
HISAT2 SRR error
srr sra alignment rna-seq hisat2 written 22 days ago by NAVID.BAVI • 0 • updated 22 days ago by genomax ♦ 58k
5
votes
1
answer
244
views
1
answer
HISAT2 Indexing using annotation for Rattus_norvegicus
hisat2 annotation alignment ensembl index written 28 days ago by neranjan • 0
0
votes
1
answer
198
views
1
answer
Is HISAT2 able to output only the best alignment?
hisat2 written 9 weeks ago by RoseString • 0 • updated 25 days ago by prasundutta87 • 260
3
votes
1
answer
225
views
1
answer
best pipeline to get gene and transcript counts
count alignment star rna-seq hisat2 written 25 days ago by lkianmehr • 30 • updated 25 days ago by t.blasco95 • 30
1
vote
0
answers
127
views
5 follow
0
answers
To fetch the reads which are being partially mapped to the genome
jvarkit hisat2 star rna-seq bowtie2 written 4 weeks ago by swadha • 20 • updated 4 weeks ago by genomax ♦ 58k
0
votes
1
answer
186
views
1
answer
Is TCGA Breast cancer data strand specific?
geneexpression tcga rna-seq strand hisat2 written 4 weeks ago by Bioinfo • 270 • updated 4 weeks ago by genomax ♦ 58k
1
vote
1
answer
95
views
1
answer
Hisat2 alignment results can be ued for TEtoolkit analysis
hisat2 tetoolkit written 4 weeks ago by lkianmehr • 30 • updated 4 weeks ago by h.mon ♦ 21k
5
votes
1
answer
172
views
1
answer
Ovation RNA-seq system, bionfomatic alignment and htseq-count
htseq-count rna-seq hisat2 written 5 weeks ago by nanoide • 10 • updated 5 weeks ago by caggtaagtat • 370
2
votes
1
answer
114
views
1
answer
Why chromosome coordinates were given for unmapped reads in hisat2?
unmapped alignment rna-seq hisat2 written 5 weeks ago by xieshaojun0621 • 90
1
vote
1
answer
123
views
1
answer
HISAT2-build killed: 9 macOS
hisat2 build rna-seq index written 6 weeks ago by datascientist28 • 350
2
votes
1
answer
206
views
1
answer
fastq file do not look as they should (running Hisat2)
fastq rna-seq hisat2 written 6 weeks ago by luzglongoria • 0
6
votes
0
answers
236
views
6 follow
0
answers
Compatibility between my reference genome and GTF file
alignment reference genome rna-seq hisat2 written 7 weeks ago by Batu • 110
5
votes
0
answers
205
views
0
answers
How to bring consistency for genome reference, annotation and index files?
genome annotation rna-seq gencode hisat2 written 7 weeks ago by Bioinfo • 270
8
votes
1
answer
262
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 7 weeks ago by shuksi1984 • 30 • updated 7 weeks ago by singh.vijender • 20
2
votes
1
answer
142
views
1
answer
How to deal with single transcripts assigned to multiple genes?
stringtie rna-seq hisat2 written 8 weeks ago by antoinefelden • 20 • updated 7 weeks ago by RamRS ♦ 19k
2
votes
1
answer
229
views
1
answer
hisat2 / bowtie: read has more quality values than read characters
bowtie2 hisat2 bowtie hisat written 8 weeks ago by juan.crescente • 20
2
votes
2
answers
186
views
5 follow
2
answers
Proper design for DESeq2 and other RNAseq general questions
stringtie deseq2 rna-seq hisat2 written 8 weeks ago by Stef • 0 • updated 8 weeks ago by swbarnes2 ♦ 4.5k
6
votes
1
answer
240
views
1
answer
Problem mapping with STAR
tophat star hisat2 written 9 weeks ago by alvarocentron91 • 0 • updated 9 weeks ago by WouterDeCoster ♦ 34k
1
vote
0
answers
204
views
0
answers
Prepare multiple gtf files for Ballgown
hisat rna-seq hisat2 written 9 weeks ago by catglen012 • 0
0
votes
0
answers
152
views
0
answers
Advantage of making HISAT2 genome index with annotation file
reference index annotations hisat2 written 9 weeks ago by piyushjo • 70 • updated 9 weeks ago by RamRS ♦ 19k
8
votes
0
answers
9.9k
views
0
answers
The comparison between HISAT2 and Tophat2
tophat2 rna-seq hisat2 written 2.7 years ago by Peng Huang • 50 • updated 10 weeks ago by RamRS ♦ 19k
0
votes
0
answers
191
views
0
answers
add read group with hisat2
algnment read group hisat2 written 3 months ago by marongiu.luigi • 330
3
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0
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983
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8 follow
0
answers
hisat2-build indexing produces more than 8 output files
indexing hisat2 written 11 months ago by ddowlin • 70 • updated 3 months ago by gaoyufeng1109 • 0
1
vote
0
answers
838
views
0
answers
Hisat2 warning: skipping mate
ngs alignment hisat2 written 16 months ago by veronicaschroeder78 • 100 • updated 3 months ago by ATpoint ♦ 9.3k
2
votes
1
answer
230
views
1
answer
Hisat2 multimapped reads
alignment rna-seq hisat2 written 3 months ago by corend • 70 • updated 3 months ago by Devon Ryan ♦ 86k
4
votes
0
answers
466
views
0
answers
hisat2 was not worked
dyld rna-seq hisat2 written 3 months ago by mikan03orange • 0
5
votes
1
answer
273
views
1
answer
Remove secondary alignments in RNA-seq analysis?
alignment rna-seq hisat2 written 4 months ago by nanoide • 10
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