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1,000 results • Page
1 of 20
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Votes
Replies
1
vote
8
replies
351
views
syntax errors when running part3 all-against-all
oma
1 hour ago by
Sofia
• 0
0
votes
0
replies
39
views
How to get BEAGLE files from VCF with angsd?
angsd
vcf
populationgenetics
beagle
pcangsd
4 hours ago by
Begonia_pavonina
▴ 90
0
votes
0
replies
60
views
How to find p-values for annotated methylated regions using methylkit and genomation
NGS
bioinformatics
pvalue
annotation
methylationarray
5 hours ago by
Saransh
• 0
2
votes
3
replies
228
views
Snakemake workflow for trimmomatic
snakemake
updated 1 hour ago by
GenoMax
127k • written 1 day ago by
antoine.fauchois92
• 0
730
votes
161
replies
109k
views
100 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 17 days ago by
Biostar
1.6k • written 6.3 years ago by
Istvan Albert
97k
0
votes
0
replies
129
views
Job:
PhD project: Analysis Of Genomics And Epigenomics Data In Mice And Humans To Clarify The Identity Of Plasmacytoid Dendritic Cells And Their Physiolog…
bioinformatics
dendritic
system
cells
immune
multiomics
10 hours ago by
aitor.gonzalez
▴ 30
1
vote
1
reply
151
views
My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
R
ENSEMBL
DESeq2
updated 15 hours ago by
GenoMax
127k • written 16 hours ago by
rgomez
• 0
0
votes
0
replies
95
views
Which ATAC-seq SAM/BAM fields are required for bigwig generation by deeptools bamCoverage?
SAM
BAM
Fields
bamCoverage
deeptools
17 hours ago by
Deep
• 0
0
votes
2
replies
169
views
Gene duplicate
monocle3
updated 19 hours ago by
ATpoint
71k • written 19 hours ago by
alghezim1
• 0
0
votes
0
replies
111
views
HiC analysis in R
R
HiC
updated 19 hours ago by
Ram
38k • written 20 hours ago by
gitprohub4
• 0
0
votes
1
reply
159
views
TCGA-BRCA tissue and RNAseq problem
NIH
RNAseq
GDC
TCGA-BRCA
updated 6 hours ago by
pinheirofabiano
▴ 10 • written 22 hours ago by
reventropy2003
• 0
0
votes
1
reply
132
views
how can i filter a sam file from a paf file
paf
sam
filter
updated 22 hours ago by
Trivas
▴ 750 • written 23 hours ago by
Mark
• 0
0
votes
1
reply
159
views
R package for functional enrichment and depletion analysis
enrichment
depletion
updated 19 hours ago by
rpolicastro
11k • written 23 hours ago by
lessismore
★ 1.3k
4
votes
2
replies
159
views
Getting Intron Positions from Amino Acid Sequences
acid
positions
amino
sequences
intron
23 hours ago by
fafad046
• 0
0
votes
0
replies
85
views
News:
New open access publication on ElasticBLAST in BMC Bioinformatics
NCBI
ElasticBLAST
BLAST
23 hours ago by
PeterC_NCBI
▴ 210
2
votes
2
replies
163
views
How to remove duplicate reads after ONT basecalling from fastq.gz files
fastq
20 hours ago by
Darrenjdd
• 0
4
votes
7
replies
240
views
What is the major problem with this pipeline of SNPs analysis?
Genomics
Fungi
SNP
VCF
updated 23 hours ago by
Ram
38k • written 1 day ago by
kgwkk2
• 0
0
votes
2
replies
138
views
Gene family classification using RNA-seq data
RNA_seq
gene_expression
gene_family
4 hours ago by
Dion
• 0
0
votes
0
replies
80
views
Seraut JackStrawplot PC1
jackstrawplot
Seurat
scRNAseq
PCA
updated 1 day ago by
Ram
38k • written 1 day ago by
miyeok
• 0
0
votes
1
reply
203
views
how can we improve genome assembly levels ? from contig to complete using bioinformatics pipelines?
contig
genome
pipelines
assembly
updated 1 day ago by
colindaven
4.6k • written 4 days ago by
vasudhapai
• 0
0
votes
1
reply
133
views
KEGG analysis in Hordeum
KEGG
vulgare
miRNA
transcripts
Hordeum
updated 23 hours ago by
GenoMax
127k • written 1 day ago by
martta95
• 0
0
votes
1
reply
116
views
""ERROR:States for individual 0 are zero " when I using GLIMPSE2 for Imputation
PBWT
imputation
gene
GLIMPSE2
updated 1 day ago by
4galaxy77
2.6k • written 1 day ago by
2013677172
• 0
0
votes
1
reply
157
views
How to run prepDE.py3?
prepDE.py3
stringtie
updated 1 day ago by
Barry Digby
★ 1.1k • written 1 day ago by
SH
• 0
0
votes
0
replies
89
views
How to interpret LASSO results for creating gene signature ?
Microarray
KM
OS
plot
1 day ago by
prithvi.mastermind
▴ 50
0
votes
0
replies
81
views
cell density scRNAseq
contourPlot
scRNAseq
1 day ago by
pingu77
▴ 10
0
votes
0
replies
70
views
fungal internal transcribed spacer metagenome (ITS)
METAGENOME
1 day ago by
Mahnoor
• 0
0
votes
0
replies
77
views
LD correlation matrix reference file, where can I find it?
ld
European
1000g
1 day ago by
Ger
• 0
0
votes
3
replies
210
views
How to deal with the probe id mapping to multiple gene ids?
match
microarray
affymetrix
probe
gene
11 hours ago by
dare_devil
★ 1.7k
0
votes
0
replies
97
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
98
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
164
views
Job:
We are looking for a bioinformatician (m/f/d) who will join our Bioinformatics Core Facility at the Max Planck Freiburg
epigenetics
sequencing
max-planck
omics
freiburg
1 day ago by
A.s.
• 0
0
votes
1
reply
123
views
Plink-association test
association
plink
case-control
covar
updated 1 day ago by
Nicolas Rosewick
10k • written 1 day ago by
Viktor Messi
• 0
5
votes
8
replies
1.5k
views
DiffBind missing peaks and FRiP
DiffBind
ChIP-seq
updated 1 day ago by
Rory Stark
★ 1.7k • written 13 months ago by
Christine
▴ 20
0
votes
1
reply
121
views
Meaning of stat values in DESeq2 result
stat
dds
result
DESeq2
updated 1 day ago by
ATpoint
71k • written 1 day ago by
woongjaej
▴ 20
2
votes
3
replies
264
views
STAR solo set parameters for scrna-seq
solo
STAR
updated 1 day ago by
colindaven
4.6k • written 3 days ago by
t.ru
▴ 20
0
votes
0
replies
113
views
Single cell RNA expression level calculation ?
scanpy
scRNA
python
1 day ago by
Athens
• 0
0
votes
0
replies
118
views
EnhancedVolcano Labels
EnhancedVolcano
R
DESeq2
1 day ago by
GA
• 0
0
votes
0
replies
122
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
4
votes
5
replies
325
views
extract gene coordinates and TSS from gene list
r
genomicranges
1 day ago by
Chironex
▴ 40
0
votes
6
replies
752
views
find the mate of a read using pysam
alignment
pysam
updated 1 day ago by
Walter
• 0 • written 3 months ago by
derealme
• 0
0
votes
0
replies
130
views
Samtools sorting
Samtools
1 day ago by
Alireza
• 0
2
votes
5
replies
266
views
best pipeline/practice for analyzing WES for germline and somatic variant calling
calling
variant
1 day ago by
epigene
▴ 580
2
votes
3
replies
267
views
ORA analysis (over-representation analysis) : different package different padjusted and qvalue
r
p-value
ORA
q-value
1 day ago by
camillab.
▴ 130
0
votes
1
reply
151
views
SKAT iniciation
SKAT
updated 1 day ago by
barslmn
★ 1.4k • written 1 day ago by
Ed
• 0
0
votes
1
reply
163
views
Difference between sratools and sratoolkit
sratools
fastq
sequencing
sratoolkit
sra
updated 1 day ago by
GenoMax
127k • written 1 day ago by
hamarillo
▴ 10
0
votes
0
replies
122
views
alelle - specific CNA/LOH
cancer
CNV
genomics
LOH
CNA
1 day ago by
Bogdan
★ 1.3k
0
votes
0
replies
141
views
Job:
Scientific Data Manager - postdoc position at ULiège, BE
Research-Storage
Scientific-Data-Management
updated 1 day ago by
Ram
38k • written 1 day ago by
jbiernaux
• 0
0
votes
0
replies
111
views
News:
Pangenomics course in April!
Pangenomics
Prokaryotic-Genomics
1 day ago by
carlopecoraro2
★ 2.3k
4
votes
6
replies
238
views
10x Cellranger SN RNA-seq BAM file output looks off
cellranger
samtools
star
bam
rna-seq
updated 1 day ago by
Ram
38k • written 1 day ago by
rebeliscu
▴ 50
0
votes
4
replies
213
views
Problem in retrieving geo data sets
geo
1 day ago by
anasjamshed
▴ 120
1,000 results • Page
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Recent Votes
C: Adjust for covariates
Comment: syntax errors when running part3 all-against-all
Picard LiftOver rejecting all Variants
Comment: pyCirclize - Circular visualization in Python
Answer: What is the major problem with this pipeline of SNPs analysis?
pyCirclize - Circular visualization in Python
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
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Recent Replies
Comment: Snakemake workflow for trimmomatic
by
GenoMax
127k
Please accept this answer (green check mark) to provide closure to this thread.
Comment: syntax errors when running part3 all-against-all
by
Sofia
• 0
When I started with the gz all-vs-all files for CHICK and ANOCA and started oma, everything ran fine, I got output. Then, in the same direc…
Comment: Quality control of Chip-seq data (NRF and PCB)
by
michelafrancesconi9
• 0
Can you explain me better? Because for the NRF I do : a) samtools view -c .bam b)samtools view -c -F 260 .bam then b/a and as a bam fi…
Comment: pyCirclize - Circular visualization in Python
by
karenkvn
▴ 40
Thank you for responding so quickly - this works perfectly!
Comment: pyCirclize - Circular visualization in Python
by
moshi
▴ 110
Please install Biopython with v1.80 or higher. If biopython>=1.80, there should be no errors.
Comment: Gene family classification using RNA-seq data
by
Dion
• 0
well, I have been given the task to retrieve gene family/categorization. I found sveral papers on family classification, but no actual pack…
Comment: pyCirclize - Circular visualization in Python
by
karenkvn
▴ 40
Thank you for this wonderful programme! I am plotting a bacterial chromosome and find that when I plot the NC_000913 chromosome using the e…
Comment: SKAT in R
by
Eliza
▴ 20
@acvill can you sujjest maybe pther tools , methods for this ? ( also for every SNP i have data how many patients had the hetro/homozygous…
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…
Comment: 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…
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