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181 results • Page
2 of 4
Sort: Rank
Rank
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Votes
Replies
0
votes
2
replies
213
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
3 days ago by
jain72744
▴ 10
6
votes
2
replies
215
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 3 days ago by
Gordon Smyth
★ 7.1k • written 3 days ago by
gBioStar5
▴ 10
2
votes
5
replies
377
views
Importing a fastq file
Fastq
updated 3 days ago by
size_t
▴ 120 • written 4 days ago by
oumo
• 0
3
votes
1
reply
189
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 2 days ago by
dthorbur
★ 1.9k • written 3 days ago by
Eren
• 0
0
votes
0
replies
147
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
3 days ago by
Aytaç
• 0
0
votes
0
replies
161
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 3 days ago by
zx8754
11k • written 3 days ago by
curious_butterfly
• 0
0
votes
0
replies
151
views
supervised admixture
supervised
admixture
3 days ago by
RT
▴ 10
2
votes
0
replies
147
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
3 days ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
411
views
Different output for read length
samtools
BAM
3 days ago by
marco.barr
▴ 100
0
votes
1
reply
357
views
Snakemake fails to find conda in PBS
snakemake
updated 3 days ago by
tim.booth
▴ 60 • written 4 weeks ago by
yixinzeng
• 0
0
votes
2
replies
210
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 2 days ago by
Ram
43k • written 3 days ago by
sainavyav22
• 0
3
votes
4
replies
291
views
Truncated metadata file report from ENA Portal API
ena
python
2 days ago by
Giulia
• 0
0
votes
0
replies
180
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
3 days ago by
Matvii Mykhailichenko
• 0
0
votes
3
replies
543
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 3 days ago by
Ram
43k • written 11 weeks ago by
maplewj
▴ 10
0
votes
5
replies
292
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
8 hours ago by
feather-W
• 0
0
votes
3
replies
282
views
bcftools - reducing to "sites-only"?
sites-only
bcftools
updated 3 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
Matthew
• 0
0
votes
1
reply
143
views
input file for alternative splicing in rmats in linux
rmats
updated 3 days ago by
Ram
43k • written 3 days ago by
Lambodarswain316
• 0
2
votes
2
replies
225
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 4 days ago by
Michael
54k • written 4 days ago by
ashaneev07
▴ 20
1
vote
1
reply
437
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 4 days ago by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 10
4
votes
3
replies
2.9k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq
picard
validatesamfile
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
Lila M
★ 1.2k
2
votes
3
replies
206
views
Nextflow: how to get the process work dir, within the process
nextflow
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
ScottDansk
▴ 10
1
vote
0
replies
131
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
4 days ago by
Shae
▴ 10
0
votes
1
reply
179
views
Enhanced Volcano-Cut off
foldchange
enhancedvolcano
updated 4 days ago by
marco.barr
▴ 100 • written 4 days ago by
odi
▴ 10
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 4 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
1
vote
1
reply
143
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 4 days ago by
andres.firrincieli
3.6k • written 4 days ago by
kacollier
▴ 30
1
vote
2
replies
1.6k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 4 days ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
0
votes
0
replies
111
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 4 days ago by
Ram
43k • written 4 days ago by
curious_butterfly
• 0
1
vote
4
replies
310
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
2 days ago by
samRayne
• 0
1
vote
3
replies
234
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 3 days ago by
GenoMax
142k • written 4 days ago by
cput
• 0
0
votes
0
replies
115
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
4 days ago by
asalimih
▴ 60
0
votes
2
replies
242
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 4 days ago by
i.sudbery
19k • written 4 days ago by
Prawesh
• 0
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 4 days ago by
Emanoelle
• 0 • written 5.7 years ago by
Elizabeth
▴ 30
0
votes
2
replies
211
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 13 hours ago by
Zhenyu Zhang
★ 1.2k • written 4 days ago by
elisheva
▴ 120
0
votes
0
replies
101
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 4 days ago by
Ram
43k • written 4 days ago by
mathavanbioinfo
▴ 90
1
vote
1
reply
269
views
Seurat V5 integration
Seurat
integration
updated 4 days ago by
Ram
43k • written 8 days ago by
starswillfade
▴ 10
0
votes
2
replies
217
views
Error in plotting PCA plot in seurat
PCA
single-cell
seurat
scRNA
RNA
updated 4 days ago by
Ram
43k • written 5 days ago by
Sumeet
• 0
0
votes
0
replies
118
views
News:
Online course: Introduction to Deep Learning
Python
Deep-Learning
Convolutional-Neural-Network
Machine-Learning
updated 4 days ago by
Ram
43k • written 4 days ago by
carlopecoraro2
★ 2.5k
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 4 days ago by
DavidStreid
▴ 90 • written 6.4 years ago by
madhu.9124
▴ 60
0
votes
2
replies
151
views
How/where can I get fungal mitogenome data for analysis?
fungal
mitogenome
updated 4 days ago by
GenoMax
142k • written 4 days ago by
madders73
• 0
4
votes
2
replies
255
views
How can I analyze normalized expression data?
DEseq2
RNA-seq
4 days ago by
mnx0723
• 0
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 4 days ago by
chloek88
• 0 • written 5.5 years ago by
Philipp Bayer
8.4k
3
votes
5
replies
347
views
RNA seq analysis
DESeq
RNA-seq
2 days ago by
prifa
▴ 10
10
votes
3
replies
305
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 5 days ago by
b.contreras.moreira
▴ 180 • written 5 days ago by
ijarne
• 0
0
votes
0
replies
141
views
Chance for trained without experience
bio
updated 5 days ago by
ATpoint
82k • written 5 days ago by
shehab
• 0
1
vote
2
replies
188
views
How do I change the title font size in ViolinPlot (Seurat)
Seurat
Violin-Plot
ggplot2
patchwork
5 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
118
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
5 days ago by
Omics data mining
▴ 260
0
votes
2
replies
176
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
5 days ago by
njornet
▴ 20
0
votes
2
replies
201
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 4 days ago by
Adam
▴ 30 • written 5 days ago by
Darya
• 0
0
votes
5
replies
246
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 4 days ago by
Joe
21k • written 5 days ago by
Lemonhope
• 0
0
votes
0
replies
172
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
4 days ago by
Winter
• 0
181 results • Page
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Recent Votes
A: Download Microarray GSE files GEO
Answer: Case and control in microarray/RNA-seq analysis
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Answer: BWA alignment
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What are chromatin states ?
Comment: Tissue-specific DEG analysis with DEseq2
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Answer: imputation through beagle
by
dthorbur
★ 1.9k
Building a reference panel from the samples you intend to impute seems like a very circular approach. Plus, GBS is a reduced representation…
Answer: Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log
by
Mensur Dlakic
★ 27k
You seem to have too stringent of a p-value cutoff (1e-5). Hopefully you get the concept of how the interplay of `-log10P-value` and `log2F…
Answer: Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log
by
yau
• 0
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Answer: Using samtools with GCS (google cloud storage) on a docker container seems to gi
by
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This is a bit late, but the first thing to go is to run `samtools --version` and make sure the docker samtools is configured with the the G…
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by
aw7
▴ 270
I do not think `samtools fixmate` and `markdup` are going to work on PacBio long reads. `fixmate` is for setting and repairing mate inform…
Comment: error in fun(x((i)), ...) : only defined on a data frame with all numeric alike
by
Azra
▴ 10
I see, thank you!
Comment: Publish a Letter in higher impact vs Research article in lower impact
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8.5k
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82k
This is off-topic here. I suggest https://academia.stackexchange.com/ Anyway, since hiring procedures in academia are much focused on IF a…
Answer: BWA alignment
by
Vahid
• 0
Thank you very much for your assistance. The problem has been solved; it was an index issue.
Answer: Manual Assembly and Protein Translation, HELP, assignment revision
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Philipp Bayer
8.4k
You asked the same question before, and I told you about the reverse complementing (https://www.biostars.org/p/9594474/#9594475 ), and now …
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Zeng Jingyu
▴ 60
Hi Nikki, I have to say that I didn't fully understand your question. You said "don't care the association between Instrumental Variable a…
Comment: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
I'm not entirely certain about the difference, but I assume it yields similar results. The method you're currently employing seems faster a…
Answer: BWA alignment
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a.alnawfal.1992
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The error [main_samview] suggests that Samtools is expecting a SAM file header but isn't getting one. This often occurs when the pipe (|) b…
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matteo.levorato
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I mean, which is the difference between doing two separated analysis or doing a one single analysis since the results are slightly differen…
Comment: How to remove multiple batch effects from RNA-seq data before limma differential
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t.fortunato.asquini
• 0
Thanks for the quick response! Yes I know that including lib.size in the design is uncommon and I have doubts about this. However, after no…
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