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510 results • Page
3 of 11
Sort: Views
Rank
Views
Votes
Replies
1
vote
2
replies
814
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 15 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
0
votes
1
reply
761
views
Low SNP Overlap with Michigan 1KG and TopMed reference panel
Michigan-Server
Phasing
TopMed
updated 29 days ago by
Ram
43k • written 12 months ago by
berndmann
▴ 10
0
votes
0
replies
737
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 13 days ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
0
votes
0
replies
736
views
"No group or design set" with deAna() function in EnrichmentBrowser package
RNA-Seq
R
EnrichmentBrowser
updated 14 days ago by
Ram
43k • written 4.1 years ago by
yxswhx
• 0
8
votes
10
replies
734
views
bash script
whole-genome-sequencing
updated 16 days ago by
Ram
43k • written 23 days ago by
bestone
▴ 30
2
votes
5
replies
708
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 11 days ago by
Jesse
▴ 740 • written 12 days ago by
Ann
★ 2.4k
2
votes
5
replies
682
views
samtools mpileup taking too long
Bam
samtools
sam
alignment
updated 26 days ago by
Ram
43k • written 7 weeks ago by
K
• 0
1
vote
0
replies
678
views
Conditions for valid batch effect correction
r
batch-effect
updated 15 days ago by
Ram
43k • written 5.2 years ago by
Sebastian Hesse
▴ 340
0
votes
1
reply
661
views
How to fix FreeBayes error "unable to find FASTA index entry for bed files"
freebayes
variant-calling
RNA-Seq
updated 29 days ago by
Ram
43k • written 13 months ago by
wlei091226
• 0
1
vote
1
reply
661
views
Save experiment with batch effects - Protein microarray
statistics
protein-array
batch-effect
updated 14 days ago by
Ram
43k • written 4.4 years ago by
s.lima.diogenes
▴ 10
0
votes
1
reply
658
views
How to find the co ordinates of long reads (simulated by Badreads) with respect to the reference genome
long-reads
reference-genome
assembly
updated 26 days ago by
Ram
43k • written 2.7 years ago by
Ashi
▴ 20
0
votes
0
replies
652
views
METAL GWAS
allele-frequency
gwas
updated 29 days ago by
Ram
43k • written 2.4 years ago by
晗颖
• 0
2
votes
6
replies
649
views
Overlapping and merging ChIP-seq peaks
MACS2
HOMER
ChIP-seq
peak-calling
updated 29 days ago by
Ram
43k • written 4 months ago by
zea
• 0
2
votes
2
replies
633
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 14 days ago by
Ram
43k • written 2.6 years ago by
Yoonji
▴ 10
0
votes
3
replies
630
views
Not all variants are annotated with AF - expected or a problem?
Variant-Calling
WGS
Alignment
updated 29 days ago by
Ram
43k • written 7 months ago by
Luiz
▴ 30
0
votes
2
replies
627
views
Seeking Alternative Tools for Predicting Mature microRNAs from Vertebrate Animal Precursors in In Silico Study
mirdeep2
maturebayes
microrna
updated 29 days ago by
Ram
43k • written 12 months ago by
Beatriz
• 0
0
votes
6
replies
618
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
differential-expression
RNA-Seq
ONT
Nanopore
updated 22 days ago by
Ram
43k • written 5 months ago by
tw_140
• 0
0
votes
4
replies
610
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
12 days ago by
Kai Xin
• 0
0
votes
9
replies
607
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 19 days ago by
LauferVA
4.2k • written 21 days ago by
Aki
▴ 20
1
vote
1
reply
599
views
accessing the global gut microbial gene catalogue (MEDUSA)
medusa
gene-catalogue
gut-microbiome
updated 20 days ago by
Ram
43k • written 3.3 years ago by
ramin.k2013
• 0
0
votes
0
replies
595
views
Avoid genome circularization with Canu assembler
circularization
ONT
Canu
repetitive-regions
assembler
updated 26 days ago by
Ram
43k • written 2.9 years ago by
Maria
• 0
4
votes
7
replies
589
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse
JBrowse2
updated 29 days ago by
cmdcolin
★ 3.8k • written 4 weeks ago by
I0110
▴ 140
4
votes
9
replies
589
views
variant calling
variant-calling
updated 28 days ago by
Ram
43k • written 29 days ago by
dalibenam64
• 0
0
votes
2
replies
580
views
Bacterial contamination in human DNA sample
Long-read-sequencing
Bacterial-contamination
updated 26 days ago by
Ram
43k • written 22 months ago by
priya.bmg
▴ 60
4
votes
7
replies
580
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 18 days ago by
Ram
43k • written 19 days ago by
AHerik
▴ 20
3
votes
12
replies
575
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
29 days ago by
Lila M
★ 1.2k
0
votes
6
replies
575
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
16 days ago by
Dunois
★ 2.5k
0
votes
5
replies
563
views
seg fault, core dumped with manta 1.6.0
manta
gdb
updated 23 days ago by
Ram
43k • written 27 days ago by
Greg
• 0
0
votes
0
replies
562
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
5 days ago by
biocellbio
• 0
0
votes
2
replies
559
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
12 days ago by
航太郎
• 0
0
votes
2
replies
555
views
autodockvina
python
python3
autodock
updated 13 days ago by
Ram
43k • written 4 months ago by
iamsmor
• 0
0
votes
1
reply
553
views
Differential Expression Analysis for miRNA
limma
Differential-gene-Expression
miRNA
updated 22 days ago by
Ram
43k • written 3.0 years ago by
Al
• 0
0
votes
11
replies
549
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
6 days ago by
atowns21
• 0
1
vote
0
replies
545
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
11 days ago by
mathavanbioinfo
▴ 90
0
votes
4
replies
542
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
13 days ago by
feather-W
• 0
1
vote
1
reply
542
views
GEO analysis with R
R
updated 29 days ago by
Ram
43k • written 2.3 years ago by
abdalla.m
• 0
0
votes
1
reply
518
views
Geneious vs Perl script of IN SILICO PCR
PCR
Geneious
updated 29 days ago by
Ram
43k • written 23 months ago by
Bio_Crap
• 0
0
votes
2
replies
516
views
Gene expression assay Yeast sample prep
Live-cells
updated 29 days ago by
Ram
43k • written 22 months ago by
dshdixit
▴ 10
2
votes
5
replies
511
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
14 days ago by
Bikram Kumar
• 0
0
votes
5
replies
505
views
How to assure that sequence consensus is genuine?
genome
25 days ago by
marongiu.luigi
▴ 710
0
votes
1
reply
488
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 6 days ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
3
votes
3
replies
486
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 11 days ago by
swbarnes2
14k • written 12 days ago by
noodle
▴ 580
1
vote
1
reply
485
views
Manta: What does all this mean
manta
Variant-calling
VEP
updated 29 days ago by
Ram
43k • written 9 months ago by
josh.mannheimer
• 0
0
votes
0
replies
480
views
How to map Uniref90 genes (IDs) to Antibiotic resistant genes databases?
CARD
metagenomics
Humann2
antibiotic-resistant-genes
uniref
updated 20 days ago by
Ram
43k • written 2.1 years ago by
ramin.k2013
• 0
0
votes
6
replies
478
views
Error in running Mauve alignner in Ubuntu 20.04
java
linux
aligner
mauve
21 days ago by
marongiu.luigi
▴ 710
2
votes
5
replies
476
views
Marking duplicates using UMIs
Deduplication
UMI
updated 9 days ago by
i.sudbery
19k • written 10 days ago by
Lipika
• 0
0
votes
10
replies
474
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 1 day ago by
i.sudbery
19k • written 9 days ago by
Patadu94
• 0
1
vote
1
reply
473
views
PLINK multivariable GLM output: p-value without BETA and SE
linear-model
glm
plink
updated 23 days ago by
chrchang523
10k • written 23 days ago by
dsbusiness135
▴ 10
0
votes
1
reply
461
views
principal coordinate analysis
PCoA
R
updated 29 days ago by
Ram
43k • written 10 months ago by
rene.j.erhardt
▴ 20
1
vote
1
reply
460
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
12 days ago by
renan.igor
• 0
510 results • Page
3 of 11
Recent Votes
C: TOPGO- how to do GO enrichment using a custom go database?
Answer: NGS forensics: how to know if data is fabricated
Comment: Adjust pvalue in R with different approach give me all different outcome
Comment: Bacterial plasmid analysis
Comment: DESeq2 processing problems
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
What Is The Difference Between Structural Variants (Svs) And Copy-Number Variants (Cnvs)?
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Recent Replies
Comment: Post-imputation plot
by
kl
▴ 10
Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
Comment: Bacterial plasmid analysis
by
GenoMax
141k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
Comment: DESeq2 processing problems
by
ATpoint
82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
Answer: Post-imputation plot
by
LChart
3.9k
I agree that some need to be flipped (A/T and C/G where your panel frequency is 1 - ref panel frequency). There are other variants which yo…
Comment: RNA editing sites based on DNA seq and RNA seq
by
Adam
▴ 30
Are those 20% unaligned reads coming after hyper-editing detection?
Answer: How to find overlap of clusters in two seurat porject
by
Adam
▴ 30
I think your best bet would be to use annotation mapping. You can use the features of your clusters in group 1 and apply them to group 2 to…
Answer: DESeq2 processing problems
by
Adam
▴ 30
> when I put in the dataset, I am not able to run it for DEG analysis because system asks me to remove the first column which is of gene na…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
Thank you so much for your quick response, I have been searching scientific papers for about a week but have failed to come up with a reaso…
Comment: Bacterial plasmid analysis
by
GenoMax
141k
> however I'm not sure this would be appropriate in my case as the plasmid sequences are obviously much more diverse and vary in size Can…
Answer: cnetplot category names are too long
by
bkleiboeker
▴ 370
I'm sure someone could find a more elegant solution using `stringr::str_wrap`, but for a one-time solution I did this: # my results of…
Comment: Telescope issue
by
GenoMax
141k
You could edit the SAM file but I wonder if this problem is present in your original fastq data file so if not inconvenient do the alignmen…
Comment: Mutect2 for mitochondria variant discovery
by
GenoMax
141k
> I keep getting error. Without providing information about the actual error no one can help. Please edit the post and add this informati…
Comment: Telescope issue
by
eleven11
• 0
Thank you! how would I correct that?
Comment: DESeq2 processing problems
by
Ram
43k
This is an open science community, not a place to write an email to Michael Love. Please address the entire community.
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