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132 results • Page
2 of 3
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Votes
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0
votes
1
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142
views
Quality control of Chip-seq data (NRF and PCB)
control
library
quality
PCB
Chip-seq
NRF
updated 2 days ago by
Darked89
4.2k • written 3 days ago by
michelafrancesconi9
• 0
0
votes
3
replies
176
views
How to deal with the probe id mapping to multiple gene ids?
match
microarray
affymetrix
probe
gene
5 hours ago by
dare_devil
★ 1.7k
0
votes
2
replies
3.8k
views
Dssp File Format?
pdb
updated 4 days ago by
Ram
38k • written 10.8 years ago by
pengcui1989
▴ 30
0
votes
0
replies
69
views
Which ATAC-seq SAM/BAM fields are required for bigwig generation by deeptools bamCoverage?
SAM
BAM
Fields
bamCoverage
deeptools
11 hours ago by
Deep
• 0
0
votes
0
replies
114
views
Problem when downloading dataset from ArrayExpress
Bioconductor
ArrayExpress
2 days ago by
cogen859
• 0
0
votes
0
replies
103
views
UK BioBank HLA imputation
ukbb
hla
imputation
2 days ago by
hla_help
• 0
0
votes
0
replies
108
views
Error at phase 4 when running GeMoMa (homology-based annotation)
Homology
GeMoMa
Annotation
Genome
3 days ago by
breannar
• 0
0
votes
3
replies
821
views
Problem to convert genotypes to plink format from bcftools
vcf
bcftools
ped
plink
beagle
updated 22 hours ago by
Manuel Ramón
▴ 10 • written 22 months ago by
Alejandro
▴ 10
0
votes
0
replies
221
views
CNVkit: setting arbitrary bin size for WGS data
CNV
CNVkit
wgs
updated 4 days ago by
Ram
38k • written 4 months ago by
ashenflower
▴ 20
0
votes
1
reply
104
views
TCGA-BRCA tissue and RNAseq problem
NIH
RNAseq
GDC
TCGA-BRCA
updated 26 minutes ago by
pinheirofabiano
▴ 10 • written 16 hours ago by
reventropy2003
• 0
0
votes
2
replies
2.7k
views
demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_strand_adapter --detect_mid_strand_barcodes produce > 90% of unclassified …
demultiplexing
guppy
2 days ago by
andres.firrincieli
3.2k
0
votes
4
replies
349
views
RNA Sequencing and Vg pan -transcriptome build
fasta
pan-transcriptome
pan-genome
vg
3 days ago by
kcarery
• 0
0
votes
0
replies
102
views
Octopus advanced vcf guide: Example of overlapping vcf calls with *
vcf
spanning
alleles
octopus
3 days ago by
penington.j
• 0
0
votes
0
replies
133
views
Link products to their genes
RNA-SEQ
GO
edgeR
4 days ago by
Pegasus
▴ 80
0
votes
0
replies
130
views
Trajectory analysis using Monocle3 with Seurat sub-clustering
scRNA-seq
Trajectory
Seurat
analysis
Monocle3
4 days ago by
joonhong kwon
▴ 40
0
votes
0
replies
128
views
how to plot distribution of SNPs across a set of genes based on distance between snp and gene
snp
genes
updated 4 days ago by
Ram
38k • written 4 days ago by
rheab1230
▴ 140
0
votes
0
replies
114
views
Reactome Species Comparison - analysis table
reactome
3 days ago by
a11msp
▴ 120
0
votes
0
replies
121
views
TrN (df = k+5) and TrNe (df = k+2) - which of these Tamura-Nei model variants is used in MEGAx?
Tamura-Nei
phylogeny
phangorn
modelTest
mega
5 days ago by
poecile.pal
▴ 50
0
votes
0
replies
172
views
How to fix FreeBayes error "unable to find FASTA index entry for bed files"
calling
freebayes
variant
RNA-Seq
6 days ago by
wlei091226
• 0
0
votes
0
replies
159
views
Emapplot Pie Graphic Legend Interferes with Map
enrichplot
clusterprofiler
Emapplot
6 days ago by
raquel.ajalik
• 0
0
votes
0
replies
172
views
ERROR using CIBERSORTx Docker version
deconvolution
version
Docker
CIBERSORTx
5 days ago by
Leite
★ 1.2k
0
votes
1
reply
192
views
doing PBS(population branch statistics) in ANGSD
fst
pbs
ANGSD
3 days ago by
Blessing
• 0
0
votes
5
replies
273
views
featureCounts problem in reading Gff
featureCounts
GFF
RNA-seq
updated 3 days ago by
Ram
38k • written 3 days ago by
Beatrice
• 0
0
votes
0
replies
103
views
Nucleotide substitution model and neighbor-joining tree
phylogeny
substitution
mega
neighbor-joining
modeltest
2 days ago by
poecile.pal
▴ 50
0
votes
0
replies
117
views
Bcftools consensus generates mismatched consensus sequence
Consensus
sequence
4 days ago by
Duy
• 0
0
votes
0
replies
262
views
Recommended tools/packages for power and sample size estimation for microRNA gene expression and/or protein expression study?
protein
sample-size
miRNA
Power
updated 4 days ago by
Ram
38k • written 9 weeks ago by
Lalaland
▴ 40
0
votes
0
replies
103
views
Michigan Imputation server failed job
michigan-imputation-server
vcf
updated 4 days ago by
Ram
38k • written 4 days ago by
Najla
• 0
0
votes
4
replies
736
views
MapSplice2 gives error if the thread count (-p value) is greater than 2
Mapsplice2
fusion_candidates
updated 4 days ago by
GenoMax
127k • written 20 months ago by
nkmalini97
• 0
0
votes
0
replies
444
views
What is a good Standardized Beta/standardized regression coefficient in a genetics study?
regression
genetics
genomics
updated 4 days ago by
Ram
38k • written 19 months ago by
jon.klonowski
▴ 130
0
votes
2
replies
285
views
LDSC correlation calculate confidence intervals
correlation
intervals
confidence
genetic
LDSC
12 hours ago by
YL
▴ 10
0
votes
0
replies
108
views
Clustering method for CT values of two group
PCA
Clustering
bioconductor
R
2 days ago by
Maria17
▴ 10
0
votes
0
replies
113
views
ABSOLUTE for tumour purity with WES
tumour-purity
ABSOLUTE
WES
updated 2 days ago by
Ram
38k • written 2 days ago by
Cvlind
• 0
0
votes
0
replies
64
views
LD correlation matrix reference file, where can I find it?
ld
European
1000g
23 hours ago by
Ger
• 0
0
votes
0
replies
61
views
fungal internal transcribed spacer metagenome (ITS)
METAGENOME
23 hours ago by
Mahnoor
• 0
0
votes
0
replies
113
views
what is the impact of 10% contamination in bacterial growth experiment in downstream analysis?
bacterial
contamination
assay
experiment
1 day ago by
eli_bayat
▴ 80
0
votes
0
replies
72
views
cell density scRNAseq
contourPlot
scRNAseq
23 hours ago by
pingu77
▴ 10
0
votes
1
reply
159
views
Using multimaping reads or unique reads on featurecounts?
featurecounts
HISAT2
updated 4 days ago by
GenoMax
127k • written 4 days ago by
omargmc.tak
• 0
0
votes
0
replies
81
views
calculation of calibration factors using impuation reference panel and ethnicity
GWAS
Calibration
factor
3 days ago by
parveenkayenat
• 0
0
votes
4
replies
416
views
Problem with fatsq-dump
fastq-dump
sratoolkit
5 days ago by
Utpal
• 0
0
votes
0
replies
87
views
kraken2 - unmapped sequences during the first step of building the database #708
metagenomics
kraken2
taxonomy
kraken
linux
1 day ago by
aziznasr1920
• 0
0
votes
0
replies
88
views
UCSC Xena browser subgroup DNA Methylation data by beta value for a specific probe
Methylation
DNA
UCSC
Xena
probe
1 day ago by
smbc
• 0
0
votes
0
replies
403
views
PSMC parameter choosing (-t, -p)
psmc
updated 4 days ago by
Ram
38k • written 20 months ago by
clinnaeus
▴ 30
0
votes
1
reply
1.6k
views
size (how many amino acids) are cytosolic or extracellular in membrane protein
protein
updated 4 days ago by
Ram
38k • written 5.6 years ago by
mabohawya
• 0
0
votes
0
replies
113
views
alelle - specific CNA/LOH
cancer
CNV
genomics
LOH
CNA
1 day ago by
Bogdan
★ 1.3k
0
votes
5
replies
553
views
Python table data extraction
python
updated 4 days ago by
Ram
38k • written 7 months ago by
deniselavezzari
• 0
0
votes
4
replies
206
views
Problem in retrieving geo data sets
geo
1 day ago by
anasjamshed
▴ 120
0
votes
0
replies
79
views
How to interpret LASSO results for creating gene signature ?
Microarray
KM
OS
plot
23 hours ago by
prithvi.mastermind
▴ 50
0
votes
1
reply
125
views
KEGG analysis in Hordeum
KEGG
vulgare
miRNA
transcripts
Hordeum
updated 17 hours ago by
GenoMax
127k • written 21 hours ago by
martta95
• 0
0
votes
1
reply
595
views
Insert size historgram from Picard for Illumina paried end 150 bp: FR, TANDEM, and both
Illumina
bam
insert-size
updated 4 days ago by
Ram
38k • written 16 months ago by
robertwhbaldwin
• 0
0
votes
2
replies
1.4k
views
Predictions of genomic breeding values using haplotypes. Softwares?
SNP
updated 1 day ago by
Ram
38k • written 7.6 years ago by
Paula Sanchez
• 0
132 results • Page
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Recent Votes
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor
SSPACE for scaffolding
Answer: Snakemake workflow for trimmomatic
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
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Comment: TCGA-BRCA tissue and RNAseq problem
by
pinheirofabiano
▴ 10
Go to https://portal.gdc.cancer.gov > Exploration > select TCGA and the cancer type you want > select case ID to download the files and hav…
Answer: Snakemake workflow for trimmomatic
by
antoine.fauchois92
• 0
Thank you very much for your reply ! It's working now !
Comment: Dependent p values
by
Eliza
▴ 20
@lchart I'm sorry for asking another of questions but I'm new to this field , can you please explain a little more how to use SKAT , saige…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
dare_devil
★ 1.7k
similar question [here][1], [here][2] and [here][3] [1]: https://support.bioconductor.org/p/54838/ [2]: https://support.bioconductor.…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
dare_devil
★ 1.7k
@genomax I have used the same platform file only. If you look at probe id and their corresponding `Gene Symbol` or `ENTREZ_GENE_ID` you can…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
GenoMax
127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned. [1]: https://www.ncbi.nlm.nih.go…
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
by
rpolicastro
11k
`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
Comment: Snakemake doesn't recognize output files even though they are created
by
DdogBoss
• 0
Yes, it completed the dry run. What other information do you need?
Comment: LDSC correlation calculate confidence intervals
by
YL
▴ 10
Based on my personal thought, I think the se from LDSC output probably needs to be transferred using Delta method based on Fisher transform…
Comment: LDSC correlation calculate confidence intervals
by
YL
▴ 10
Hi, Are you able to find an answer for this? I have the exact question! YL
Answer: Gene duplicate
by
ATpoint
71k
Use use ensembID_geneName as gene identifier to avoid that. These duplicate names exist as genes so removing them is somewhat not really da…
Comment: Gene duplicate
by
Ram
38k
> some Ensembl IDs that are the same Please show us some examples.
Comment: R package for functional enrichment and depletion analysis
by
rpolicastro
11k
What you're describing is a simulation of the hypergeometric test, so if you want an exact solution you could use the function `fora` from …
Comment: How to remove duplicate reads after ONT basecalling from fastq.gz files
by
Darrenjdd
• 0
Perfect! Thank you!
Comment: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
by
Daniel
• 0
Hi, I am wondering if you ever got an answer for this question. Also, I am curious why it is true that "All the reads coming from one end…
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