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396 results • Page
4 of 8
Sort: replies
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Views
Votes
Replies
0
votes
2
replies
366
views
GSEA analysis in R
GSEA
R
Arabidopsis
27 days ago by
Sudip
• 0
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 27 days ago by
Ram
43k • written 6.6 years ago by
Alternative
▴ 290
0
votes
2
replies
310
views
RNAseq 1 control 2 different treatment
RNA-seq
29 days ago by
matteo.levorato
• 0
0
votes
2
replies
171
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
1 day ago by
IdaHao0921
• 0
0
votes
2
replies
339
views
How to update R on ubuntu
installation
update
R
apt-get
16 days ago by
Bosberg
▴ 50
0
votes
2
replies
309
views
Annovar using R package
Annovar
gnomAD
R
20 days ago by
DKA
▴ 40
0
votes
1
reply
699
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 14 days ago by
Ram
43k • written 15 days ago by
Dr Huma Naz
• 0
0
votes
1
reply
1.2k
views
Controlling for batch effect in SNP-based PCA
whole-genome
PCA
batch-effect
SNP
updated 28 days ago by
Ram
43k • written 4.8 years ago by
Ace
▴ 90
0
votes
1
reply
158
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 7 days ago by
Bastien Hervé
5.3k • written 8 days ago by
sooni
▴ 20
0
votes
1
reply
199
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 5 days ago by
Ram
43k • written 5 days ago by
Shwetha
• 0
0
votes
1
reply
145
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 1 day ago by
GenoMax
142k • written 1 day ago by
bioinfo
▴ 150
0
votes
1
reply
302
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 26 days ago by
GenoMax
142k • written 26 days ago by
bioyas
▴ 10
0
votes
1
reply
205
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 21 days ago by
Sofia
• 0 • written 21 days ago by
mawigoj318
• 0
0
votes
1
reply
195
views
Differential Accessibility
DiffBind
updated 16 days ago by
Ram
43k • written 16 days ago by
Shloka
• 0
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca
ruvseq
sva
svaseq
batch-effect
updated 28 days ago by
Ram
43k • written 6.3 years ago by
jjrin
▴ 40
0
votes
1
reply
125
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
20 hours ago by
sansan_96
▴ 90
0
votes
1
reply
153
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 2 days ago by
GenoMax
142k • written 2 days ago by
cedric.blais
• 0
0
votes
1
reply
601
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 13 days ago by
mdav
• 0 • written 19 months ago by
Zoe
• 0
0
votes
1
reply
211
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 22 days ago by
bk11
★ 2.4k • written 22 days ago by
alphaflylizard
• 0
0
votes
1
reply
1.8k
views
Advice required for remove batch effect which perfectly collinear with contrast of interest
RNA-seq
batch-effect
updated 27 days ago by
Ram
43k • written 6.7 years ago by
boymin2020
▴ 80
1
vote
1
reply
134
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 1 day ago by
Ram
43k • written 1 day ago by
kilcdincer
▴ 10
0
votes
1
reply
173
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 14 days ago by
Ram
43k • written 14 days ago by
ernestine.kubi
• 0
0
votes
1
reply
249
views
Subsetting and merging back Seurat Object brings different results
Seurat
13 days ago by
Bine
▴ 60
1
vote
1
reply
522
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
26 days ago by
renan.igor
• 0
0
votes
1
reply
296
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 8 days ago by
andres.firrincieli
3.6k • written 9 days ago by
Antonio
• 0
1
vote
1
reply
264
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 20 days ago by
ATpoint
82k • written 20 days ago by
AaronJaime
• 0
0
votes
1
reply
79
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
8 hours ago by
asalimih
▴ 60
0
votes
1
reply
209
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 22 days ago by
bk11
★ 2.4k • written 22 days ago by
Susmita Mandal
▴ 110
0
votes
1
reply
234
views
Help with DGEList function
DGEList
R
updated 10 days ago by
marco.barr
▴ 120 • written 11 days ago by
Natali
• 0
0
votes
1
reply
227
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 14 days ago by
GenoMax
142k • written 14 days ago by
mgranada3
▴ 30
0
votes
1
reply
199
views
RNA-seq bacteria contamination
RNA-seq
updated 23 days ago by
GenoMax
142k • written 23 days ago by
sh
• 0
0
votes
1
reply
228
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 28 days ago by
DKA
▴ 40 • written 28 days ago by
james.melhorn
• 0
1
vote
1
reply
453
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 24 days ago by
Gordon Smyth
★ 7.2k • written 27 days ago by
Chris
▴ 280
0
votes
1
reply
306
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 28 days ago by
GenoMax
142k • written 28 days ago by
ycts
• 0
1
vote
1
reply
172
views
student
epitranscriptomics
updated 8 days ago by
ATpoint
82k • written 8 days ago by
useriwa
• 0
0
votes
1
reply
1.2k
views
Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
random-effects
RNA-Seq
batch-effect
updated 28 days ago by
Ram
43k • written 6.8 years ago by
Dipro
• 0
3
votes
1
reply
204
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 5 days ago by
dthorbur
★ 2.0k • written 6 days ago by
Eren
• 0
0
votes
1
reply
211
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 11 days ago by
Ram
43k • written 12 days ago by
Valentina
• 0
1
vote
1
reply
253
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 15 days ago by
Ram
43k • written 15 days ago by
Jonathan Yoou
▴ 60
0
votes
1
reply
842
views
How to compare differentially expressed genes among different affymatrix dataset
microarray
batch-effect
R
updated 28 days ago by
Ram
43k • written 4.8 years ago by
Calangoa
▴ 30
0
votes
1
reply
174
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 23 days ago by
Ram
43k • written 23 days ago by
Cameron.walker9900
• 0
1
vote
1
reply
156
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 13 days ago by
Ram
43k • written 13 days ago by
marco.barr
▴ 120
0
votes
1
reply
222
views
Freyja plot error
Freyja
updated 28 days ago by
Ram
43k • written 28 days ago by
Adyasha
• 0
0
votes
1
reply
833
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 27 days ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
1
vote
1
reply
667
views
Save experiment with batch effects - Protein microarray
statistics
protein-array
batch-effect
updated 28 days ago by
Ram
43k • written 4.4 years ago by
s.lima.diogenes
▴ 10
0
votes
1
reply
158
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 23 days ago by
ATpoint
82k • written 23 days ago by
enanoide
• 0
0
votes
1
reply
238
views
Finding batch and outlayers
Pca
updated 16 days ago by
christopher medway
▴ 460 • written 17 days ago by
Tigran
• 0
0
votes
1
reply
88
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 8 hours ago by
yura.grabovska
▴ 70 • written 8 hours ago by
ev97
▴ 20
0
votes
1
reply
155
views
How to process Bulk WES data?
WES
WGS
updated 2 days ago by
GenoMax
142k • written 2 days ago by
wyuan37
• 0
0
votes
1
reply
560
views
HOMER on AWS
HOMER
updated 12 days ago by
clairechung112
• 0 • written 2.3 years ago by
Bogdan
★ 1.4k
396 results • Page
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Comment: bbmerge (bbmap) ~ error with insert size file output
by
chrisk
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Hi Brian, Thank you and apologies for the extra future revision works. Out of curiosity we disabled neural networks 'nn=f' and the file o…
Comment: bbmerge (bbmap) ~ error with insert size file output
by
chrisk
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Hi Genomax, This is the thread: https://www.biostars.org/p/9582467/ Cheers, Chris
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that's helpful, thanks :)
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These are valid questions. Does your code address the concerns you've raised? From what I understand, FilterVcf is primarily designed for h…
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