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895 results • Page
3 of 18
Sort: replies
Rank
Views
Votes
Replies
1
vote
7
replies
482
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
12 days ago by
eebloom
▴ 80
7
votes
7
replies
6.0k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 20 days ago by
rohitsatyam102
▴ 860 • written 6.2 years ago by
smallfish
▴ 10
3
votes
7
replies
392
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
16 days ago by
salias
• 0
6
votes
7
replies
368
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
3 days ago by
sansan_96
▴ 90
0
votes
7
replies
621
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 12 days ago by
LChart
3.9k • written 16 days ago by
kl
▴ 10
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 4 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
3
votes
7
replies
553
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq
tmt
nomenclature
proteomics
29 days ago by
ntsopoul
▴ 60
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon
human
bed
v7
agilent
all
sureselect
updated 10 days ago by
MiladAD
▴ 10 • written 2.0 years ago by
soheil
• 0
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient
molecule
at
bam
DNA
RG
ends
clipping
damage
updated 7 days ago by
chenl
▴ 10 • written 2.5 years ago by
Martyna
• 0
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 27 days ago by
colindaven
6.4k • written 10.9 years ago by
Ontheway
▴ 10
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 9 days ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
4
votes
6
replies
798
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 18 days ago by
dsull
★ 6.0k • written 22 days ago by
qudrat.nii
▴ 10
0
votes
6
replies
467
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 12 days ago by
swbarnes2
14k • written 12 days ago by
Erina
• 0
1
vote
6
replies
718
views
anRichment is missing
WGCNA
anRichment
updated 9 days ago by
GenoMax
142k • written 6 months ago by
michael.flower.14
▴ 180
0
votes
6
replies
492
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 21 days ago by
gv
• 0 • written 6 weeks ago by
Srinka
▴ 20
0
votes
6
replies
399
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 1 day ago by
Ram
43k • written 4 days ago by
ajbarrett98
• 0
2
votes
6
replies
3.7k
views
Algorithm to remove batch effects
single-cell
batch-effect
RNA-Seq
updated 28 days ago by
Ram
43k • written 3.3 years ago by
fouerghi20
▴ 80
1
vote
6
replies
506
views
Rename multiple fastq.gz files
fastq
next-gen
updated 29 days ago by
shenwei356
8.5k • written 29 days ago by
Jérémie
• 0
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray
meta-analysis
DEG
batch-effect
updated 28 days ago by
Ram
43k • written 4.9 years ago by
mosesoo
▴ 30
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 16 days ago by
dimpleadiwal050896
• 0 • written 5.0 years ago by
ggman
▴ 90
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 18 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
5
votes
6
replies
581
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 15 days ago by
me
▴ 760 • written 16 days ago by
Mariana
▴ 40
3
votes
6
replies
8.4k
views
RNA-seq, EdgeR and batch effects
RNA-Seq
removeBatchEffect
edgeR
batch-effect
updated 28 days ago by
Ram
43k • written 9.4 years ago by
Ekarl2
▴ 120
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray
r
GEOquery
updated 28 days ago by
Ram
43k • written 5.0 years ago by
mosesoo
▴ 30
2
votes
6
replies
5.3k
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 27 days ago by
Ram
43k • written 3.8 years ago by
Lukadon77
• 0
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov
scatter-plot
anova
updated 28 days ago by
Ram
43k • written 3.2 years ago by
Rob
▴ 170
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 15 days ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
2
votes
6
replies
360
views
BWA alignment
Samtools
bam
updated 14 hours ago by
a.alnawfal.1992
▴ 260 • written 2 days ago by
Vahid
• 0
4
votes
6
replies
538
views
Odd results with BLAST remote
blast
remote
NCBI
updated 29 days ago by
b.contreras.moreira
▴ 180 • written 4 weeks ago by
Begonia_pavonina
▴ 150
3
votes
6
replies
11k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 29 days ago by
Bioinfotec
▴ 10 • written 7.6 years ago by
nut_B
▴ 10
3
votes
6
replies
907
views
Any problem re-using last year's RNA-Seq data in this year's analysis?
RNA-Seq
batch-effect
updated 28 days ago by
Ram
43k • written 3.8 years ago by
oakhamwolf
▴ 20
3
votes
6
replies
479
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 2 days ago by
Pine
▴ 20 • written 10 days ago by
snajafy
• 0
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 27 days ago by
John Marshall
3.0k • written 2.0 years ago by
bioguy24
▴ 230
4
votes
6
replies
4.0k
views
Correcting for batch effect in RNA-seq data
RNA-Seq
batch-effect
updated 28 days ago by
Ram
43k • written 4.8 years ago by
Rimma
▴ 30
0
votes
6
replies
443
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
22 days ago by
Sd
• 0
10
votes
6
replies
10k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 19 days ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 520
2
votes
6
replies
3.8k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 20 days ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
3
votes
6
replies
748
views
Ciriquant not configuring hisat2 indexed files
ciriquant
23 days ago by
Atul K.
• 0
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 6 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
1
vote
6
replies
387
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 12 days ago by
GenoMax
142k • written 4 weeks ago by
eebloom
▴ 80
2
votes
6
replies
890
views
Batch effect correction with cell type enrichment analysis
limma
RNA-seq
r
batch-effect
updated 28 days ago by
Ram
43k • written 19 months ago by
JACKY
▴ 140
7
votes
6
replies
581
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
24 days ago by
analyst
▴ 50
3
votes
6
replies
2.5k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 28 days ago by
Ram
43k • written 22 months ago by
ev97
▴ 20
1
vote
6
replies
1.8k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
entrez direct
ncbi
XML format
updated 39 minutes ago by
Ash
• 0 • written 3.9 years ago by
millere
• 0
0
votes
5
replies
323
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
2 days ago by
feather-W
• 0
2
votes
5
replies
2.9k
views
Batch effect in Axiom Human Origins Array
affymetrix
array
batch-effect
updated 28 days ago by
Ram
43k • written 7.9 years ago by
Simo
▴ 50
1
vote
5
replies
804
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 26 days ago by
BioinfGuru
★ 1.7k • written 27 days ago by
rrehimi
• 0
4
votes
5
replies
446
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
16 days ago by
analyst
▴ 50
2
votes
5
replies
477
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 23 hours ago by
Ram
43k • written 7 days ago by
Prawesh
• 0
3
votes
5
replies
1.8k
views
Limma/edgeR Design matrix for gender effect
RNA-Seq
batch-effect
updated 28 days ago by
Ram
43k • written 4.7 years ago by
kailsen
• 0
895 results • Page
3 of 18
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Answer: Filtering VCF files based on VAF giving incorrect results
Problems with breakdancer (sv caller) output.
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Answer: In one PCA plot, can I calculate the percentage of different factors that contri
by
marco.barr
▴ 110
Hi, regardless of how you generated the data whether with DESeq2 or other pipeline, your differential expression matrix can be used as inpu…
Comment: Filtering VCF files based on VAF giving incorrect results
by
Pierre Lindenbaum
161k
> Do you think my commands were correct? I'm not familiar enough with this bcftools syntax. but what if there is no AD, what if both…
Answer: How can you *consistently* download BioProject IDs from NCBI's BioSample databas
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Ash
• 0
I know this was asked several years ago, but finding this post helped me solve my own problem and in the process I solved this one too. …
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Would Parkinson's be expected to have an effect on blood cells? Neurons, sure, but blood cells?
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by
MarcosCosta
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Thank you very much, you've helped me a lot. Could you suggest a book or article that offers a complete explanation of these processes?
Comment: Filtering VCF files based on VAF giving incorrect results
by
Arton
• 0
Thank you. I can't try a completely new tool but I will keep your command for future use. Do you think my commands were correct? For exampl…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Thanks. Thats work
Comment: Genotyping sites with N in reference genome
by
Zhenyu Zhang
★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 110
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Pierre Lindenbaum
161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome
by
Pierre Lindenbaum
161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
yura.grabovska
▴ 70
Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
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asalimih
▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
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