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Showing top results for tag:
rna-seq
•
reset
0
votes
2
replies
35
views
[E::idx_find_and_load] Could not retrieve index file for 'xxxxxsorted.bam'
rna-seq
2 hours ago by
jenyfer
• 0
1
vote
1
reply
101
views
Make New Orig.ident in seurat object or
R
RNA-SEQ
Seurat
updated 15 hours ago by
fracarb8
▴ 140 • written 15 hours ago by
Maria17
• 0
6
votes
13
replies
432
views
single tumor vs multiple normal sample differential gene expression (RNA-Seq ) analysis using DESeq2
RNA-Seq
DESeq2
updated 5 hours ago by
ATpoint
48k • written 1 day ago by
sumitguptabt
▴ 10
1
vote
2
replies
81
views
hisat2 output from paired en reads.
hisat2
rna-seq
updated 2 days ago by
Zhilong Jia
★ 1.7k • written 2 days ago by
Palgrave
▴ 30
3
votes
1
reply
79
views
Understanding the ColData Matrix
RNA-SEQ
R
Micheal_Love
DESEQ2
updated 2 days ago by
jared.andrews07
9.3k • written 2 days ago by
raisamathenge
▴ 30
0
votes
1
reply
123
views
GDC Data Query
RNA-Seq
updated 2 days ago by
Zhenyu Zhang
▴ 280 • written 4 weeks ago by
p20170409
• 0
1
vote
1
reply
2.3k
views
How to design WGCNA: one analysis over all sample or seperate analysis (using consensus module analysis)?
WGCNA
RNA-seq
updated 2 days ago by
Kevin Blighe
72k • written 4 days ago by
leesooyeon94
▴ 10
1
vote
1
reply
85
views
Normalisation before edgeR for RNA-Seq
rna-seq
edgeR
updated 4 days ago by
ATpoint
48k • written 4 days ago by
ZheFrench
▴ 320
0
votes
1
reply
251
views
comparing enriched GO terms between species
RNA-Seq
go
annotation
updated 4 days ago by
babalyigit
• 0 • written 9 months ago by
martinaweil
• 0
0
votes
1
reply
160
views
Canu transcriptome assembly behavior
nanopore
RNA-Seq
canu
updated 5 days ago by
vgilbart
• 0 • written 12 weeks ago by
chrys
▴ 40
2
votes
7
replies
13k
views
6 follow
HISAT error: Encountered internal HISAT2 exception (#1)
RNA-Seq
updated 5 days ago by
Federico Giorgi
▴ 640 • written 3.9 years ago by
pixie@bioinfo
★ 1.4k
2
votes
2
replies
104
views
Deseq2 time interaction term
deseq2
rna-seq
DE
R
updated 5 days ago by
swbarnes2
9.7k • written 5 days ago by
townsendae
• 0
0
votes
4
replies
208
views
Prinseq lite data preprocessing
Data
rna-seq
preprocessing
Forum
Prinseq
lite
updated 5 days ago by
Ram
32k • written 3 months ago by
Adarsh Kuamr
▴ 40
1
vote
3
replies
163
views
How to get GO terms to specific to perticular biological process
GO
Enrichment
RNA-seq
updated 5 days ago by
geneticatt
▴ 120 • written 7 days ago by
BISEP
• 0
15
votes
10
replies
544
views
How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
transcript
rna-seq
updated 5 days ago by
tamerg
▴ 90 • written 8 days ago by
Quanyou
• 0
0
votes
3
replies
198
views
How to interpret multiqc report
QC
multiqc
rna-seq
updated 1 day ago by
Phil Ewels
▴ 620 • written 6 days ago by
townsendae
• 0
2
votes
5
replies
175
views
Plotting Differential Induced Genes across timepoints in DESEQ2
Bioconductor
MA
RNA-seq
DESEQ2
3 days ago by
raisamathenge
▴ 30
0
votes
2
replies
106
views
correlation analysis of a single variable versus multiple variables
correlation
r
RNA-Seq
6 days ago by
pinheirofabiano
• 0
4
votes
6
replies
280
views
Batch effect correction of 2 studies with different covariates
batch-effect
R
RNA-seq
updated 5 days ago by
Dunois
▴ 630 • written 7 days ago by
Geo
▴ 20
0
votes
0
replies
72
views
integration of single cell RNA-seq and bulk RNA-seq data
RNA-seq
7 days ago by
ramyak1912
• 0
0
votes
0
replies
48
views
Minimum enrichment score to take for analysis
Sequencing
Rna-Seq
7 days ago by
ashwing.kofficial
• 0
1
vote
4
replies
1.1k
views
Can't change coefficient of dds object: error 'coef' should specify same coefficient as in results 'res'
DESeq2
RNA-seq
3 days ago by
macielrodriguez2
▴ 30
66
votes
38
replies
21k
views
22 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
rna-seq
bioconductor
fpkm
Forum
Tutorial
updated 7 days ago by
vel
• 0 • written 7.5 years ago by
Irsan
★ 7.3k
1
vote
3
replies
229
views
how remove large gene ontology terms from gprofiler2 output
gprofiler2
GO
DEseq
RNA-seq
updated 6 days ago by
jared.andrews07
9.3k • written 7 days ago by
BISEP
• 0
1
vote
3
replies
158
views
How do I find the gene name with the allele number from the databases?
rna-seq
updated 7 days ago by
GenoMax
99k • written 7 days ago by
Rasoulfarzaneh63
• 0
7
votes
12
replies
493
views
RNAseq data analysis of pooled data
DESeq2
mapping
featurecounts
clustering
RNA-Seq
updated 1 day ago by
grant.hovhannisyan
★ 2.1k • written 8 days ago by
luffy
▴ 20
0
votes
0
replies
60
views
CPM or TPM values as discretization method input
RNA-Seq
discretization
TPM
CPM
8 days ago by
antmantras
• 0
3
votes
4
replies
305
views
Expression of gene of interest across conditions in single-cell data
singlecell
scater
tpm
seurat
Rna-seq
7 days ago by
kz
• 0
4
votes
6
replies
331
views
Creating reference genome for mapping and then selecting
mm10
hg38
STAR
RNA-seq
updated 8 days ago by
Istvan Albert
87k • written 9 days ago by
Dataminer
★ 2.7k
0
votes
1
reply
148
views
Extracting transcripts from whole-transcriptome libraries
galaxy
vcf
rna-seq
updated 9 days ago by
GenoMax
99k • written 9 days ago by
julianneradford
• 0
0
votes
0
replies
1.3k
views
In KisSplice, I already set "ulimit -s unlimited", but I am still getting stack limit error. Is there a work around this?
snp
kissplice
rna-seq
stack
KisSplice
9 days ago by
ec-ho-ra-mos
• 0
0
votes
0
replies
50
views
Could it be risky to analyse cells that are negative after cell hashing on single cell RNA sequencing?
RNA-Seq
singlecell
R
Seurat
10 days ago by
charlesgwellem
• 0
5
votes
7
replies
291
views
Data normalization
normalization
RNA-seq
10 days ago by
nolwenn
▴ 10
0
votes
1
reply
183
views
Seurat obj conversion to Anndata not accurately creating var in a h5ad file
RNA-Seq
R
Seurat
Anndata
10 days ago by
akh22
▴ 50
0
votes
2
replies
135
views
How to use deseq 2 file for keggscape in cytoscape
RNA-SEQ
Visualization
Sequencing
Cytoscape
9 days ago by
ashwing.kofficial
• 0
1
vote
1
reply
154
views
Identifying gene sequence in RNA-Seq data
sequence
genomic
rna-seq
alignment
10 days ago by
snow4964
▴ 10
0
votes
3
replies
211
views
WGCNA Timepoint Analysis
WGCNA
rna-seq
celltypes
updated 11 days ago by
Kevin Blighe
72k • written 11 days ago by
sujitsilas
• 0
11
votes
7
replies
5.3k
views
6 follow
Automatic Outlier Detection for RNA-seq data
RNA-Seq
outlier
rrcov
updated 11 days ago by
Melisa
▴ 10 • written 3.5 years ago by
JJ
▴ 560
16
votes
4
replies
11k
views
6 follow
Volcano plot p-value or FDR?
RNA-Seq
updated 12 days ago by
dariober
12k • written 4.9 years ago by
balestrieri.c
▴ 70
1
vote
2
replies
181
views
Comparing Log2 Fold Change Values across all timepoints between two groups in DESEQ2
RNA-seq
Bioconductor
DESEQ2
R
updated 12 days ago by
Carlo Yague
5.8k • written 12 days ago by
raisamathenge
▴ 30
0
votes
4
replies
264
views
Plotting points that are in Enhanced Volcano that are 0.01 LFC units apart
RNA-seq
EnhancedVolcano
6 days ago by
raisamathenge
▴ 30
3
votes
7
replies
1.6k
views
Tophat2 Error gzip pipe broken? zipped file empty?
tophat2
RNA-Seq
gzip
bowtie
alignment
updated 12 days ago by
1589537403
• 0 • written 2.8 years ago by
biogirl04
▴ 10
3
votes
8
replies
292
views
Quantification of stranded RNA-seq data
featureCounts
RNA-seq
stranded
Hisat2
updated 12 days ago by
Carlo Yague
5.8k • written 12 days ago by
Rogerio Ribeiro
▴ 50
2
votes
6
replies
325
views
Aligning Paired-end file in R/Rstudio using align function
Rstudio
RNA-Seq
R
updated 12 days ago by
colindaven
★ 2.7k • written 15 days ago by
student
• 0
8
votes
6
replies
484
views
How to select genes with multi-exon 3'UTR
rna-seq
genome
gff
gene
updated 13 days ago by
Juke34
★ 5.4k • written 16 days ago by
tianshenbio
▴ 90
1
vote
3
replies
180
views
How to get DNA and RNA datasets from GEO,TCGA and EBI
dna-seq
Genome
rna-seq
13 days ago by
Milan
• 0
0
votes
2
replies
147
views
How to install PEER in R?
PEER
R
Rstudio
RNA-Seq
13 days ago by
sahar.salimi92
• 0
0
votes
3
replies
163
views
Package to predict genomic variants from rna-seq read data
Genomics
rna-seq
13 days ago by
dk0319
▴ 20
0
votes
0
replies
61
views
how to build a graph reference with HISAT-genotype
reference
RNA-seq
hisat2
alignment
14 days ago by
minghuiguo448
• 0
2
votes
4
replies
1.2k
views
ELI5: Different methods to analyse differential expression other than limma?
RNA-Seq
microarray
affymetrix
limma
updated 14 days ago by
ATpoint
48k • written 4.8 years ago by
ruslanovna.kim
▴ 10
50 results • Page
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TCGA patient variable data dictionary
Answer: TMM-Normalization
Iterating through paired-end reads in samtools / pysam
Answer: TMM-Normalization
Answer: Bam File: Change Chromosome Notation
Answer: Future of Microarrays
Answer: TMM-Normalization
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Recent Replies
Comment: Create Mutational signature plot from vcf file.
by
nhaus
▴ 30
Unfortunately, it does not seem like this tool outputs this particular plot.
Comment: Convertion Of Gff3 To Gtf
by
daalsa98
▴ 10
Oh, thanks!, I'll take a look and see if it works
Answer: Convertion Of Gff3 To Gtf
by
lieven.sterck
11k
you can have a look at the AGAT toolkit https://www.biostars.org/p/413510/ , there might be some tool in it that can do this.
Answer: Bam File: Change Chromosome Notation
by
Pierre Lindenbaum
135k
update 2021: I wrote http://lindenb.github.io/jvarkit/ConvertBamChromosomes.html
Answer: Future of Microarrays
by
GenoMax
99k
Arrays remain alive. Demise of arrays has been predicted for a few years but they continue to be used since they are a proven technology. D…
Answer: Create Mutational signature plot from vcf file.
by
amitpande74
▴ 20
tried this ? [comutplotter][1] [1]: http://tardis.cgu.edu.tw/comutplotter/
Comment: DiffBind consensus peak extraction
by
wei.zhang
• 0
Hi Rory, here is the information > sessionInfo() R version 4.0.5 (2021-03-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu …
Comment: Can't count features with featurecount
by
Michael Dondrup
48k
That is a bit weird, so you cannot get around a QC. I suspect that your mRNA is degraded due to storage as FFPE and therefore only few read…
Comment: Skewed Betweenness Centrality values resulting in almost unusable PPI networks f
by
gemmalouisebaldock
▴ 20
Thank you for the response, may I just ask for clarification. 1) Are you saying that a solution could be to change my mapping from 0-0.7, …
Comment: [E::idx_find_and_load] Could not retrieve index file for 'xxxxxsorted.bam'
by
jenyfer
• 0
thanks but it still gives the same error `[E::idx_find_and_load] Could not retrieve index file for '/mnt/d/RNA-SEQ/SRR13532540/SRR13532540s…
Comment: Converting Braker2 gtf output to gff then genbank
by
Juke34
★ 5.4k
Yes with an awk command throw out all lines with gene and transcript feature type (3rd column). Then reconstruct them by runing `agat_conve…
Answer: [E::idx_find_and_load] Could not retrieve index file for 'xxxxxsorted.bam'
by
ATpoint
48k
Index it: `samtools index your.bam`
Comment: R and GEO
by
ATpoint
48k
First step is adding details. Which dataset?
Comment: Converting Braker2 gtf output to gff then genbank
by
robert.murphy
▴ 40
The plan is to use them for [antiSMASH][1]. Do you mean to filter out any line the the feature gene and transcript string? [1]: https:…
Comment: genomicdbImport issue
by
ijlal.hyder2012
▴ 10
Hi, Thanks for your response. Just curious if this will speed it up since my interval list is only 400000 bps (which isnt that big)? second…
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