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16,563 results • Page
1 of 332
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Filtering for tag:
RNA-Seq
•
reset
0
votes
1
reply
30
views
Normalisation before edgeR for RNA-Seq
rna-seq
edgeR
updated 2 hours ago by
ATpoint
48k • written 3 hours ago by
ZheFrench
▴ 320
0
votes
1
reply
227
views
comparing enriched GO terms between species
RNA-Seq
go
annotation
updated 3 hours ago by
babalyigit
• 0 • written 9 months ago by
martinaweil
• 0
0
votes
0
replies
793
views
How to design WGCNA: one analysis over all sample or seperate analysis (using consensus module analysis)?
WGCNA
RNA-seq
9 hours ago by
leesooyeon94
• 0
0
votes
1
reply
147
views
Canu transcriptome assembly behavior
nanopore
RNA-Seq
canu
updated 1 day 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 1 day ago by
Federico Giorgi
▴ 640 • written 3.9 years ago by
pixie@bioinfo
★ 1.4k
2
votes
2
replies
77
views
Deseq2 time interaction term
deseq2
rna-seq
DE
R
updated 1 day ago by
swbarnes2
9.7k • written 1 day ago by
townsendae
• 0
0
votes
4
replies
196
views
Prinseq lite data preprocessing
Data
rna-seq
preprocessing
Forum
Prinseq
lite
updated 1 day ago by
Ram
32k • written 3 months ago by
Adarsh Kuamr
▴ 40
1
vote
3
replies
133
views
How to get GO terms to specific to perticular biological process
GO
Enrichment
RNA-seq
updated 1 day ago by
geneticatt
▴ 120 • written 3 days ago by
BISEP
• 0
15
votes
10
replies
490
views
How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
transcript
rna-seq
updated 1 day ago by
tamerg
▴ 90 • written 4 days ago by
Quanyou
• 0
0
votes
2
replies
148
views
How to interpret multiqc report
QC
multiqc
rna-seq
2 days ago by
townsendae
• 0
2
votes
5
replies
139
views
Plotting Differential Induced Genes across timepoints in DESEQ2
Bioconductor
DESEQ2
MA
RNA-seq
updated 2 days ago by
swbarnes2
9.7k • written 2 days ago by
raisamathenge
▴ 10
0
votes
2
replies
87
views
correlation analysis of a single variable versus multiple variables
correlation
r
RNA-Seq
2 days ago by
pinheirofabiano
• 0
4
votes
6
replies
239
views
Batch effect correction of 2 studies with different covariates
batch-effect
R
RNA-seq
updated 1 day ago by
Dunois
▴ 620 • written 3 days ago by
Geo
▴ 20
0
votes
0
replies
61
views
integration of single cell RNA-seq and bulk RNA-seq data
RNA-seq
3 days ago by
ramyak1912
• 0
0
votes
0
replies
36
views
Minimum enrichment score to take for analysis
Sequencing
Rna-Seq
3 days ago by
ashwing.kofficial
• 0
1
vote
3
replies
1.0k
views
Can't change coefficient of dds object: error 'coef' should specify same coefficient as in results 'res'
DESeq2
RNA-seq
updated 2 days ago by
ATpoint
48k • written 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 3 days ago by
vel
• 0 • written 7.5 years ago by
Irsan
★ 7.3k
1
vote
3
replies
191
views
how remove large gene ontology terms from gprofiler2 output
gprofiler2
GO
DEseq
RNA-seq
updated 2 days ago by
jared.andrews07
9.2k • written 3 days ago by
BISEP
• 0
1
vote
3
replies
145
views
How do I find the gene name with the allele number from the databases?
rna-seq
updated 3 days ago by
GenoMax
99k • written 3 days ago by
Rasoulfarzaneh63
• 0
5
votes
10
replies
324
views
RNAseq data analysis of pooled data
DESeq2
mapping
featurecounts
clustering
RNA-Seq
4 hours ago by
luffy
▴ 20
0
votes
0
replies
54
views
CPM or TPM values as discretization method input
RNA-Seq
discretization
TPM
CPM
4 days ago by
antmantras
• 0
3
votes
4
replies
282
views
Expression of gene of interest across conditions in single-cell data
singlecell
scater
tpm
seurat
Rna-seq
3 days ago by
kz
• 0
4
votes
6
replies
299
views
Creating reference genome for mapping and then selecting
mm10
hg38
STAR
RNA-seq
updated 4 days ago by
Istvan Albert
87k • written 5 days ago by
Dataminer
★ 2.7k
0
votes
1
reply
134
views
Extracting transcripts from whole-transcriptome libraries
galaxy
vcf
rna-seq
updated 5 days ago by
GenoMax
99k • written 5 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
5 days ago by
ec-ho-ra-mos
• 0
0
votes
0
replies
40
views
Could it be risky to analyse cells that are negative after cell hashing on single cell RNA sequencing?
RNA-Seq
singlecell
R
Seurat
6 days ago by
charlesgwellem
• 0
5
votes
7
replies
252
views
Data normalization
normalization
RNA-seq
6 days ago by
nolwenn
▴ 10
0
votes
1
reply
170
views
Seurat obj conversion to Anndata not accurately creating var in a h5ad file
RNA-Seq
R
Seurat
Anndata
6 days ago by
akh22
▴ 50
0
votes
2
replies
122
views
How to use deseq 2 file for keggscape in cytoscape
RNA-SEQ
Visualization
Sequencing
Cytoscape
5 days ago by
ashwing.kofficial
• 0
1
vote
1
reply
143
views
Identifying gene sequence in RNA-Seq data
sequence
genomic
rna-seq
alignment
6 days ago by
snow4964
▴ 10
0
votes
3
replies
189
views
WGCNA Timepoint Analysis
WGCNA
rna-seq
celltypes
updated 7 days ago by
Kevin Blighe
72k • written 7 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 7 days ago by
Melisa
▴ 10 • written 3.4 years ago by
JJ
▴ 560
16
votes
4
replies
11k
views
6 follow
Volcano plot p-value or FDR?
RNA-Seq
updated 8 days ago by
dariober
12k • written 4.9 years ago by
balestrieri.c
▴ 70
1
vote
2
replies
162
views
Comparing Log2 Fold Change Values across all timepoints between two groups in DESEQ2
RNA-seq
Bioconductor
DESEQ2
R
updated 8 days ago by
Carlo Yague
5.8k • written 8 days ago by
raisamathenge
▴ 10
0
votes
4
replies
235
views
Plotting points that are in Enhanced Volcano that are 0.01 LFC units apart
RNA-seq
EnhancedVolcano
2 days ago by
raisamathenge
▴ 10
3
votes
7
replies
1.6k
views
Tophat2 Error gzip pipe broken? zipped file empty?
tophat2
RNA-Seq
gzip
bowtie
alignment
updated 8 days ago by
1589537403
• 0 • written 2.8 years ago by
biogirl04
▴ 10
3
votes
8
replies
253
views
Quantification of stranded RNA-seq data
featureCounts
RNA-seq
stranded
Hisat2
updated 8 days ago by
Carlo Yague
5.8k • written 8 days ago by
Rogerio Ribeiro
▴ 50
2
votes
6
replies
293
views
Aligning Paired-end file in R/Rstudio using align function
Rstudio
RNA-Seq
R
updated 8 days ago by
colindaven
★ 2.7k • written 11 days ago by
student
• 0
8
votes
6
replies
455
views
How to select genes with multi-exon 3'UTR
rna-seq
genome
gff
gene
updated 9 days ago by
Juke34
★ 5.3k • written 12 days ago by
tianshenbio
▴ 90
1
vote
3
replies
166
views
How to get DNA and RNA datasets from GEO,TCGA and EBI
dna-seq
Genome
rna-seq
9 days ago by
Milan
• 0
0
votes
2
replies
126
views
How to install PEER in R?
PEER
R
Rstudio
RNA-Seq
9 days ago by
sahar.salimi92
• 0
0
votes
3
replies
146
views
Package to predict genomic variants from rna-seq read data
Genomics
rna-seq
9 days ago by
dk0319
▴ 20
0
votes
0
replies
53
views
how to build a graph reference with HISAT-genotype
reference
RNA-seq
hisat2
alignment
10 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 10 days ago by
ATpoint
48k • written 4.8 years ago by
ruslanovna.kim
▴ 10
0
votes
1
reply
95
views
How to convert an RDS file containing annotated cells to a loom file
R
Scanpy
RNA-seq
updated 12 days ago by
rpolicastro
5.1k • written 12 days ago by
Olalekan
• 0
3
votes
6
replies
6.7k
views
Calculating fpkm from raw counts
RNA-Seq
R
fpkm
updated 12 days ago by
Ahmed Alhendi
▴ 70 • written 3.0 years ago by
vinayjrao
▴ 200
0
votes
0
replies
66
views
using RNAseq reads to verify predicted gene models
prediction
gene
RNA-seq
12 days ago by
sullis02
• 0
2
votes
4
replies
264
views
What are the disadvantages of increasing the sequencing depth of RNA-seq experiment?
NGS
RNA-Seq
sequencing
depth
transcriptome
12 days ago by
mrj
▴ 20
0
votes
0
replies
62
views
SortmeRNA error
SortmeRNA
RNA-seq
updated 13 days ago by
GenoMax
99k • written 13 days ago by
pallob.barai
• 0
0
votes
5
replies
319
views
How to use the goseq for ensemble gene ID
RNA-SEQ
R
annotations
GO
11 days ago by
BISEP
• 0
16,563 results • Page
1 of 332
Recent Votes
convert fasta/gb to vcf
Parallel haplotyping
Comment: Meaning letters in TCGA sample barcode field
Comment: Meaning letters in TCGA sample barcode field
Answer: MASURCA error for multiple entries
Comment: Finding how many times a nucleotide appear in the same position
Normalization of ATAC SEQ data for the proper deeptools heatmap
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Comment: big loss after markduplication
by
reza
▴ 250
Now, after deletion of duplicated reads, What is the problem if I want to use this data for the analyzes I mentioned earlier (SNP calling, …
Comment: Download all Bacteria accession list from NCBI
by
GenoMax
99k
AFAIK `datasets` is only meant to work with genome level data. Doing ./datasets download genome taxon 2 will get you information abou…
Comment: Download all Bacteria accession list from NCBI
by
GenoMax
99k
If you have access to `nr` blast database then use `blastdbcmd` which is part of `blast+` package. blastdbcmd -db nr -taxids 2 -outfmt…
Comment: Download all Bacteria accession list from NCBI
by
GenoMax
99k
A lot of records are going to be `WP*` accessions which point to multiple organisms. Something to keep in mind.
Comment: Download all Bacteria accession list from NCBI
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A related Python script that you could use (search by FASTA title): https://www.biostars.org/p/279584/#279811
Comment: short length amino acids
by
GenoMax
99k
> Can anybody help me how to blast them locally ? You can install `blast` program locally and use that. BLAST Handbook from NCBI: https://…
Comment: Meaning letters in TCGA sample barcode field
by
Kevin Blighe
72k
You are welcome, Sumit.
Comment: Precision of variant calling (INDELs)
by
desouzareis.r
▴ 220
Hi, yes it could. You can compare coverage between them, especially in regions where there are false positive and false negative variants r…
Comment: hello ever one
by
GenoMax
99k
Biostars does not have an `Introductions` tradition. I don't want to delete this post because it may ban your account. Please do not post t…
Comment: Meaning letters in TCGA sample barcode field
by
sumitguptabt
• 0
Thank you so much @kevin I will look into it and update you ASAP. BW Sumit
Comment: MASURCA error for multiple entries
by
Kevin Blighe
72k
Great to hear - thank you.
Comment: Meaning letters in TCGA sample barcode field
by
Kevin Blighe
72k
Hi, you can search for these here: https://portal.gdc.cancer.gov/ They seem to be from Clinical Proteomic Tumor Analysis Consortium (CPTAC)
Comment: GATK 4 and Spark multithreading
by
Victoria
• 0
I am sorry, I didn't realise that wasn't allowed, I have deleted the other post.
Comment: Meaning letters in TCGA sample barcode field
by
sumitguptabt
• 0
@krushnach80 Thank you, dear, These samples are from: cancer types: bronchus and lung, subtype: adenomas and adenocarcinomas. The data is H…
Comment: Meaning letters in TCGA sample barcode field
by
krushnach80
▴ 910
what samples are these which tissue type?
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