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181 results • Page
2 of 4
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2
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147
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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
408
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
209
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
289
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
542
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 3 days ago by
Ram
43k • written 11 weeks ago by
maplewj
▴ 10
0
votes
5
replies
261
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
3 hours ago by
feather-W
• 0
0
votes
3
replies
281
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
142
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
220
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 3 days ago by
Michael
54k • written 4 days ago by
ashaneev07
▴ 20
1
vote
1
reply
436
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 3 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 3 days ago by
Pierre Lindenbaum
161k • written 3 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 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
ScottDansk
▴ 10
1
vote
0
replies
129
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
3 days ago by
Shae
▴ 10
0
votes
1
reply
179
views
Enhanced Volcano-Cut off
foldchange
enhancedvolcano
updated 3 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 3 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
1
vote
1
reply
142
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 3 days ago by
andres.firrincieli
3.6k • written 3 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
110
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
0
votes
0
replies
114
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
3 days ago by
Zeng Hao
▴ 40
1
vote
4
replies
306
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
2 days ago by
rackbersingh
• 0
1
vote
3
replies
231
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
240
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 3 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
200
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 7 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
266
views
Seurat V5 integration
Seurat
integration
updated 4 days ago by
Ram
43k • written 7 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 4 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
253
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
344
views
RNA seq analysis
DESeq
RNA-seq
2 days ago by
prifa
▴ 10
10
votes
3
replies
301
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 4 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 4 days ago by
ATpoint
82k • written 4 days ago by
shehab
• 0
1
vote
2
replies
187
views
How do I change the title font size in ViolinPlot (Seurat)
Seurat
Violin-Plot
ggplot2
patchwork
4 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
117
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
4 days ago by
Omics data mining
▴ 260
0
votes
2
replies
174
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
4 days ago by
njornet
▴ 20
0
votes
2
replies
199
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 4 days ago by
Adam
▴ 30 • written 4 days ago by
Darya
• 0
0
votes
5
replies
241
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 4 days ago by
Joe
21k • written 4 days ago by
Lemonhope
• 0
0
votes
0
replies
170
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
3 days ago by
Winter
• 0
0
votes
5
replies
291
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
4 days ago by
me
• 0
2
votes
1
reply
134
views
java out of memory error through beagle for imutation
beagle
java.out.of.memory
imputation
4 days ago by
analyst
▴ 50
0
votes
0
replies
83
views
Blog:
Introduction to The Complete Sequence of a Human Genome
biotech
5 days ago by
usa.cd.genomics
• 0
0
votes
0
replies
90
views
Blog:
Overview of Nanopore Sequencing
biotech
5 days ago by
usa.cd.genomics
• 0
0
votes
0
replies
102
views
meffil.snp.concordance
meffil
methylation
snp_concordance
5 days ago by
kyj222637
• 0
0
votes
1
reply
146
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 4 days ago by
Bastien Hervé
5.3k • written 5 days ago by
sooni
▴ 20
181 results • Page
2 of 4
Recent Votes
Answer: Server or aws cloud- which one is better for gatk pipeline
Comment: How to remove multiple batch effects from RNA-seq data before limma differential
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automatic clustering annotation using python
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C: Convert .Txt File To Bed File
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rj.rezwan
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colindaven
6.4k
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pjb39
▴ 200
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Jen
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Answer: CNVKIT - unable to produce scatter and diagram pdfs
by
Anitha
• 0
While running with this batch option batch --method wgs option. I have used this command " cnvkit.py batch tumor.bam -n normal.bam -m wgs -…
Answer: Generating .bed file and .map file for polyploid vcf file through plink
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10k
Why do you think ADMIXTURE supports polyploid input? (Note that this is an answer, not a comment.)
Comment: How to convert normalized BigWig file to count matrix?
by
feather-W
• 0
Hi ATpoint, Thanks for your reply!
Comment: How to convert normalized BigWig file to count matrix?
by
feather-W
• 0
Hi Pierre, Thanks for your reply! I want to get a feature count matrix from coverage data stored in BigWig files. And this BigWig file ha…
Comment: Extracting mutation status from MAF files - TCGA
by
Zhenyu Zhang
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you can assume all genes without mutation is WT (easy) while controlling for (difficult) - coverage - capture region - germline - the …
Comment: Obtaining Infinium Methylation450K manifest for hg38
by
Zhenyu Zhang
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Since you are getting data from the GDC, analysis-related reference/annotations can be found in the GDC reference page here https://gdc.can…
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fracarb8
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I saw that, but considering that your analysis is in seurat and that both liana and liana+ are from the same developers, it might be quicke…
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You can rank normalize them, but to tell the truth, I won't trust any conclusion you can draw from such combined data. The recommended …
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Include confounders into the limma design. No need for upfront removal. Note that libsize is taken care of by normalizing usually. Are you …
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Thank you very much, success in your projects.
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Thanks for the input :)
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This seems to indicate that the package itself (or packages it depends on) are not compatible with the R version you are using. Next step c…
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Not my area of expertise but GTEx portal seems to offer visual comparison of expression across tissues, maybe checking their pipeline could…
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> I think I am mostly struggling with what would need to be coded to my dataset here and how to run this loop on my set in general. i do…
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by
ajbarrett98
• 0
Pierre, I am a novice at all of this in general and I have never used Java-based programming before. I may not be able to properly wrangl…
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