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1,000 results • Page
4 of 20
Sort: replies
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Views
Votes
Replies
0
votes
6
replies
291
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
1 day ago by
Sd
• 0
8
votes
6
replies
614
views
The bioinformatics paper reappears, but the results are significantly different from the original results
reproducibility
20 days ago by
jiao
▴ 40
3
votes
6
replies
891
views
Any problem re-using last year's RNA-Seq data in this year's analysis?
RNA-Seq
batch-effect
updated 8 days ago by
Ram
43k • written 3.7 years ago by
oakhamwolf
▴ 20
15
votes
6
replies
1.3k
views
6 follow
VCF to human friendly form?
vcf
visualization
updated 10 days ago by
Pierre Lindenbaum
161k • written 19 months ago by
wormball
▴ 10
8
votes
6
replies
2.5k
views
Batch effect removal with the help of sva
SVA
batch-effect
gene-expression
updated 17 days ago by
Ram
43k • written 3.5 years ago by
Gene_MMP8
▴ 240
2
votes
6
replies
630
views
Overlapping and merging ChIP-seq peaks
MACS2
HOMER
ChIP-seq
peak-calling
updated 23 days ago by
Ram
43k • written 4 months ago by
zea
• 0
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma
sva
batch-effect
R
updated 10 days ago by
Ram
43k • written 3.8 years ago by
amirmehrgou
▴ 10
11
votes
6
replies
514
views
Pangenome of plant
pangenome
plant
17 days ago by
analyst
▴ 30
4
votes
6
replies
832
views
bwa mem hangs after a few thousand reads
bwa
alignment
variant-calling
bwa-mem
updated 23 days ago by
Ram
43k • written 4 months ago by
cee28
▴ 30
2
votes
6
replies
451
views
KEGG analysis in R
KEGG
clusterProfiler
Zea-mays
14 days ago by
sansan_96
▴ 80
0
votes
6
replies
457
views
Error in running Mauve alignner in Ubuntu 20.04
java
linux
aligner
mauve
15 days ago by
marongiu.luigi
▴ 710
5
votes
6
replies
391
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot
RNAseq
Rstudio
updated 23 days ago by
Istvan Albert
100k • written 24 days ago by
Pumla
• 0
4
votes
6
replies
2.0k
views
RNA-Seq DGE: Evaluate model quality
differential-gene-expression
RNA-Seq
deseq2
updated 16 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
0
votes
6
replies
424
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 1 day ago by
gv
• 0 • written 24 days ago by
Srinka
▴ 20
0
votes
6
replies
613
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
differential-expression
RNA-Seq
ONT
Nanopore
updated 16 days ago by
Ram
43k • written 4 months ago by
tw_140
• 0
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 7 days ago by
colindaven
6.4k • written 10.9 years ago by
Ontheway
▴ 10
9
votes
6
replies
1.5k
views
What in silico PCR commandline tool do you use that can handle IUPAC characters?
pcr
amplicon
primer
updated 23 days ago by
Ram
43k • written 16 months ago by
O.rka
▴ 710
7
votes
6
replies
458
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
4 days ago by
analyst
▴ 30
1
vote
6
replies
415
views
Rename multiple fastq.gz files
fastq
next-gen
updated 8 days ago by
shenwei356
8.4k • written 9 days ago by
Jérémie
• 0
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov
scatter-plot
anova
updated 8 days ago by
Ram
43k • written 3.2 years ago by
Rob
▴ 170
2
votes
6
replies
861
views
Batch effect correction with cell type enrichment analysis
limma
RNA-seq
r
batch-effect
updated 8 days ago by
Ram
43k • written 19 months ago by
JACKY
▴ 140
2
votes
6
replies
3.7k
views
Algorithm to remove batch effects
single-cell
batch-effect
RNA-Seq
updated 8 days ago by
Ram
43k • written 3.3 years ago by
fouerghi20
▴ 80
2
votes
6
replies
567
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
21 days ago by
Lissa Cruz Saavedra
• 0
2
votes
6
replies
5.2k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq
R
seurat
harmony
batch-effect
updated 7 days ago by
Ram
43k • written 3.7 years ago by
Lukadon77
• 0
3
votes
6
replies
1.5k
views
edgeR FDR always 1
FDR
differential-gene-expression
edgeR
miRNA
updated 16 days ago by
Ram
43k • written 4.9 years ago by
AngAdd
▴ 20
4
votes
6
replies
1.4k
views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlength…
gff3
GenomicRanges
ORFik
GenomicFeatures
updated 10 days ago by
GenoMax
141k • written 15 months ago by
Estefania
▴ 30
2
votes
6
replies
399
views
create a gene count matrix csv file from seurat object
Seurat
sparseMatrix
17 days ago by
jkim
▴ 170
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 7 days ago by
John Marshall
3.0k • written 24 months ago by
bioguy24
▴ 230
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray
meta-analysis
DEG
batch-effect
updated 8 days ago by
Ram
43k • written 4.8 years ago by
mosesoo
▴ 30
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 8 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
0
votes
6
replies
548
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
10 days ago by
Dunois
★ 2.5k
6
votes
6
replies
4.3k
views
10x to cloupe
single-cell-transcriptomics
10x
16 days ago by
firestar
★ 1.6k
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq
batch-effect
updated 8 days ago by
Ram
43k • written 4.8 years ago by
Rimma
▴ 30
4
votes
6
replies
443
views
Odd results with BLAST remote
blast
remote
NCBI
updated 9 days ago by
b.contreras.moreira
▴ 170 • written 10 days ago by
Begonia_pavonina
▴ 150
3
votes
6
replies
11k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 9 days ago by
Bioinfotec
▴ 10 • written 7.6 years ago by
nut_B
▴ 10
5
votes
5
replies
848
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq
Blacklist
updated 13 days ago by
Ram
43k • written 10 months ago by
Emily Wasson
▴ 30
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq
countOverlaps
R
updated 8 days ago by
Ram
43k • written 6.3 years ago by
seta
★ 1.9k
3
votes
5
replies
1.3k
views
How to identify antibiotic resistant genes in gene databases?
antibiotic
Gene-Ontology
GO
updated 14 days ago by
Ram
43k • written 2.0 years ago by
ramin.k2013
• 0
0
votes
5
replies
416
views
Error running local blastn in R using system2
blastn
NCBI
R
27 days ago by
Harrison
• 0
1
vote
5
replies
1.0k
views
Align short sequence against ONT reads
long-reads
ONT
alignment
genome
updated 20 days ago by
Ram
43k • written 22 months ago by
kirillkirilenko
▴ 40
2
votes
5
replies
477
views
Creating an index from multiple .fsa files
HISAT2
BWA
Alignment
16 days ago by
theworldsagainstme
• 0
0
votes
5
replies
333
views
BUSCO analysis failed due to Duplicate of sequence in Input genome fasta. How to solve this problem ?
duplicate
BUSCO.
updated 21 days ago by
GenoMax
141k • written 21 days ago by
Sony
▴ 10
2
votes
5
replies
2.8k
views
Batch effect in Axiom Human Origins Array
affymetrix
array
batch-effect
updated 8 days ago by
Ram
43k • written 7.9 years ago by
Simo
▴ 50
2
votes
5
replies
668
views
samtools mpileup taking too long
Bam
samtools
sam
alignment
updated 20 days ago by
Ram
43k • written 6 weeks ago by
K
• 0
0
votes
5
replies
377
views
Parsing fasta file by coordinates
linux
fasta
updated 28 days ago by
GenoMax
141k • written 4 weeks ago by
sorrymouse
▴ 120
0
votes
5
replies
289
views
How to compare bulk RNA seq data demultiplexed in different ways?
RNA-seq
updated 20 days ago by
Ram
43k • written 24 days ago by
bioinfo
▴ 150
37
votes
5
replies
13k
views
How do you generate TMM normalized counts using EdgeR?
R
RNA-seq
edgeR
updated 15 days ago by
inedraylig
▴ 60 • written 2.9 years ago by
Pratik
★ 1.0k
1
vote
5
replies
587
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode
MGI
DNBelab
single-cell
updated 2 days ago by
atowns21
• 0 • written 3 months ago by
benjamin.pyenson
• 0
1
vote
5
replies
1.5k
views
Blastn in galaxy
Blastn
galaxy
updated 23 days ago by
Ram
43k • written 3.0 years ago by
adnan.lahuf
• 0
1
vote
5
replies
1.5k
views
How to correct unknown Batch effect?
PCA
gene-expression
DESeq2
RNA-seq
batch-effect
updated 8 days ago by
Ram
43k • written 12 months ago by
luffy
▴ 110
1,000 results • Page
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Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Answer: How do I get the 3bp sequence on either side of a co-ordinate
What is the difference between HaplotypeCaller and UnifiedGenotyper?
What is the difference between HaplotypeCaller and UnifiedGenotyper?
RSeQC Output from infer_experiment.py - what does it mean?
ScRNAseq-How to correctly choose cell type marker genes
ScRNA data question
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Answer: why renaming Idents in Seurat object doesn't work?
by
Bioinfotec
▴ 10
I think when you give indent to seuObj : Idents(seuObj) <- 'RNA_snn_res.0.1' You may wrongly assign other value to it such as …
Answer: ScRNAseq-How to correctly choose cell type marker genes
by
Bioinfotec
▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
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by
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In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
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141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
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I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification
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82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
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ginellegrenier
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Hi, I was wondering if you have found a solution to this? Thanks!
Comment: PCA plot
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cross posted in bioconductor. [https://support.bioconductor.org/p/9157968/][1] [1]: https://support.bioconductor.org/p/9157968/
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by
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Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
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I think the coverage could also computed from bam file itself, but let say I do not include the coverage, do you have any idea why it needs…
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I am moving my answer to a comment. At this point you should email NCBI help desk and ask them this question. If you get an answer then ple…
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the javascript in your html is deprecated or your firefox is just tool old.
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> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
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