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Showing :
questions
0
votes
0
replies
157
views
rMATS reports zero evenets?
splicing
RNA-Seq
rmats
5 weeks ago by
PK
▴ 130
0
votes
0
replies
147
views
How to calculate weighted transcript length for each gene?
salmon
tximport
rna-seq
updated 6 weeks ago by
Ram
43k • written 6 weeks ago by
PK
▴ 130
2
votes
2
replies
280
views
Error from cgat gtf2gtf --method=genes-to-unique-chunks
RNA-Seq
GTF
cgat
9 weeks ago by
PK
▴ 130
4
votes
5
replies
588
views
Featurecounts has more reads than star assigned reads ?
featurecounts
STAR
RNA-seq
3 months ago by
PK
▴ 130
2
votes
1
reply
391
views
How to normalize intron counts?
DESeq
limma
RNA-SEQ
updated 10 months ago by
Asaf
10k • written 10 months ago by
PK
▴ 130
1
vote
8
replies
1.2k
views
Is it possible to use salmon alevin tool for total rna seq samples?
salmon
alignment
10 months ago by
PK
▴ 130
1
vote
1
reply
424
views
weird behaviour on bedtools
bedtools
RNA-Seq
updated 11 months ago by
Ram
43k • written 11 months ago by
PK
▴ 130
1
vote
0
replies
484
views
How to calculate Exon-Intron junction perbase coverage?
RNA-Seq
bedtools
13 months ago by
PK
▴ 130
0
votes
0
replies
358
views
Reference book for clip seq analysis?
RNASEQ
clipseq
R
14 months ago by
PK
▴ 130
0
votes
0
replies
351
views
How to normalize the counts when you are looking at 3'UTR?
bedtools
RNA-Seq
updated 10 months ago by
Ram
43k • written 15 months ago by
PK
▴ 130
0
votes
2
replies
721
views
Metagene for first last and intermediate exons?
ggplot
Rna-seq
deeptools
r
updated 10 months ago by
Ram
43k • written 16 months ago by
PK
▴ 130
0
votes
1
reply
973
views
how to create a metagene plot for different features of genes?
metagene
RNA-Seq
deeptools
R
updated 16 months ago by
seidel
11k • written 16 months ago by
PK
▴ 130
3
votes
3
replies
625
views
How to plot that the certain exons are affected in the genebody?
RNA-seq
updated 17 months ago by
Ram
43k • written 17 months ago by
PK
▴ 130
1
vote
1
reply
474
views
How to handle multiple overlap and choose closest one?
RNA-Seq
bedtools
updated 17 months ago by
Pierre Lindenbaum
161k • written 17 months ago by
PK
▴ 130
5
votes
16
replies
2.7k
views
How to extract intron counts from total RNA Sequencing?
featurecounts
RNAseq
htseq
STAR
17 months ago by
PK
▴ 130
4
votes
7
replies
1.6k
views
What is the advantage of mapping RNA-Seq against genome?
RNA-SEQ
mapping
18 months ago by
PK
▴ 130
0
votes
0
replies
373
views
can i use repeat masker gff file to directly extract the counts from fastq files?
repeat
base
masker
rep
19 months ago by
PK
▴ 130
0
votes
0
replies
328
views
How to generate gene body coverage plot for tRNA?
clipseq
peak-calling
RNA-seq
samtools
updated 10 months ago by
Ram
43k • written 21 months ago by
PK
▴ 130
0
votes
4
replies
786
views
What is the maximum size of fasta file i can use for repeatmasker?
RNAseq
Repeatmasker
repititive
elements
22 months ago by
PK
▴ 130
3
votes
11
replies
1.5k
views
RepeatMasker error
repeatmasking
transciptome
RNA-seq
updated 22 months ago by
mark.ziemann
★ 1.9k • written 22 months ago by
PK
▴ 130
1
vote
1
reply
489
views
Where to find terra (telomeric RNA) coordinates?
rnaseq
Alignment
mapping
updated 22 months ago by
Giovanni M Dall'Olio
28k • written 22 months ago by
PK
▴ 130
1
vote
2
replies
744
views
How to integrate multi omics data in cytoscape
cytoscape
protein-protein
interaction
network
22 months ago by
PK
▴ 130
2
votes
1
reply
508
views
Is it possible to find the mutation in RNA-seq reads?
RNA-seq
mapping
clip-seq
updated 2.0 years ago by
Carlo Yague
8.7k • written 2.0 years ago by
PK
▴ 130
1
vote
1
reply
482
views
where can i find all TE elements GTF?
peakcalling
RNAseq
clipseq
updated 2.2 years ago by
Michael
54k • written 2.2 years ago by
PK
▴ 130
0
votes
2
replies
554
views
Piranha peak calling waring message?
RNA-seq
peak-calling
piranha
updated 23 months ago by
Ram
43k • written 2.2 years ago by
PK
▴ 130
0
votes
2
replies
572
views
How to subset peaks based on RNA sub class?
peakcalling
RNAseq
clipseq
2.3 years ago by
PK
▴ 130
0
votes
2
replies
642
views
How to do the peak calling for introns?
RNAseq
clipseq
peakcalling
2.3 years ago by
PK
▴ 130
0
votes
0
replies
430
views
How to analyse RNA-based protein pulldown mass spectrometry data
proteomics
R
maxquant
limma
2.9 years ago by
PK
▴ 130
0
votes
1
reply
803
views
How can i handle the multimapped reads?
assembly
sequencing
alignment
updated 2.9 years ago by
Charlene Hsuan-lin Her
• 0 • written 3.2 years ago by
PK
▴ 130
1
vote
1
reply
478
views
Extract co-ordinate for iCLIP data?
sequencing
linux
RNA
updated 2.9 years ago by
Istvan Albert
100k • written 2.9 years ago by
PK
▴ 130
5
votes
6
replies
3.5k
views
How to calculate per base coverage from the .bam file?
RNA-Seq
next-gen
R
updated 4.6 years ago by
ATpoint
82k • written 4.6 years ago by
PK
▴ 130
0
votes
3
replies
1.4k
views
Export error WITH AGP?
software error
genome
next-gen
alignment
updated 4.6 years ago by
Jonathanjacobs
▴ 280 • written 6.9 years ago by
PK
▴ 130
0
votes
0
replies
669
views
how to define more stringent parameters for the snoscan to indentify snoRNA target on rRNA?
sequence
rna-seq
genome
4.8 years ago by
PK
▴ 130
1
vote
3
replies
1.0k
views
How to extract un annotated (With abundant) small RNA transcript?
RNA-Seq
sequencing
Assembly
updated 5.3 years ago by
GouthamAtla
12k • written 5.3 years ago by
PK
▴ 130
17
votes
13
replies
15k
views
8 follow
duplicate 'row.names' are not allowed
RNA-Seq
software error
R
updated 5.3 years ago by
paul.boisseaux
▴ 10 • written 5.9 years ago by
PK
▴ 130
1
vote
2
replies
2.0k
views
multicuv error Could not find indexes
RNA-Seq
alignment
software error
updated 5.9 years ago by
Nitin Narwade
★ 1.6k • written 5.9 years ago by
PK
▴ 130
2
votes
4
replies
5.0k
views
memory is low reading termination?
RNA-Seq
alignment
next-gen
updated 6.0 years ago by
GenoMax
142k • written 6.0 years ago by
PK
▴ 130
3
votes
6
replies
2.5k
views
how to find new transcript from bam file?
next-gen
alignment
RNA-Seq
updated 6.0 years ago by
Federico Giorgi
▴ 730 • written 6.0 years ago by
PK
▴ 130
1
vote
4
replies
1.5k
views
Any possible to run cuffdiff without cuffqunt?
RNA-Seq
software error
next-gen
updated 6.7 years ago by
Biostar
20 • written 7.2 years ago by
PK
▴ 130
3
votes
8
replies
5.6k
views
How to import reference genome in CLC genomics workbench?
software error
next-gen
genome
updated 6.9 years ago by
lakhujanivijay
5.8k • written 6.9 years ago by
PK
▴ 130
0
votes
4
replies
1.9k
views
Installation error with funannotate?
RNA-Seq
software error
alignment
next-gen
6.9 years ago by
PK
▴ 130
5
votes
8
replies
2.3k
views
How to preform genome annotation?
next-gen
alignment
genome
updated 6.9 years ago by
Rohit
★ 1.5k • written 6.9 years ago by
PK
▴ 130
0
votes
0
replies
1.6k
views
How to specify frag len mean and frag len std dev while running cufflinks?
RNA-Seq
software error
next-gen
updated 7.1 years ago by
Biostar
20 • written 7.3 years ago by
PK
▴ 130
1
vote
1
reply
942
views
What is difference between default mode and with parameter mode in HTSeq?
RNA-Seq
htseq
ngs
7.1 years ago by
PK
▴ 130
4
votes
8
replies
3.2k
views
How to identify adapters in FASTQ file?
RNA-Seq
fastqc
ngs
updated 7.2 years ago by
WouterDeCoster
47k • written 7.2 years ago by
PK
▴ 130
0
votes
4
replies
880
views
Data replicating error?
RNA-Seq
ngs
software error
7.2 years ago by
PK
▴ 130
11
votes
9
replies
11k
views
How calculate RPKM values for DESeq?
R
RNA-Seq
software error
updated 7.2 years ago by
ddiez
★ 2.0k • written 7.2 years ago by
PK
▴ 130
6
votes
5
replies
1.9k
views
DESeq error of my data?
R
RNA-Seq
software error
7.2 years ago by
PK
▴ 130
6
votes
4
replies
2.5k
views
I got error when i run DESeq None of your conditions is replicated. Use method='blind' to estimate across conditions, or 'pooled-CR', if you have cr…
R
RNA-Seq
software error
updated 7.2 years ago by
ddiez
★ 2.0k • written 7.2 years ago by
PK
▴ 130
0
votes
0
replies
1.2k
views
Which parameters to change in Tophat default settings for homosapiens cancer data?
RNA-Seq
next-gen
software error
7.2 years ago by
PK
▴ 130
58 results • Page
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