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110,388 results • Page
1 of 2208
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0
votes
0
replies
1
view
how to sort a fasta file
fasta
sort
just now by
Mohd
• 0
0
votes
1
reply
26
views
Single Cell Rna Seq Using BD Rhapsody
Rhapsody
BD
updated 1 hour ago by
GenoMax
129k • written 1 hour ago by
abbas.waseem.gcu
• 0
0
votes
0
replies
11
views
The inchworm process failed. Trinity running error.
error
inchworm
transcriptome
trinity
1 hour ago by
Marta
• 0
0
votes
3
replies
49
views
ggsave() bug in ggplot2?
ggplot2
ggsave
updated just now by
barslmn
★ 1.5k • written 2 hours ago by
Medeea
• 0
0
votes
2
replies
34
views
DEGseq for multiple samples
DEGexp
DEGseq
6 minutes ago by
ALOUSH ALI
• 0
1
vote
3
replies
66
views
BioInformatics, Software
BioInformatics
Learning
Softwares
1 hour ago by
hashim.rana11
• 0
743
votes
162
replies
113k
views
101 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 weeks ago by
Biostar
1.8k • written 6.5 years ago by
Istvan Albert
98k
1
vote
1
reply
44
views
How to calculate kinship matrix table from vcf file
variants
haplotyping
kinship
heatmap
updated 1 hour ago by
barslmn
★ 1.5k • written 2 hours ago by
rj.rezwan
• 0
1
vote
1
reply
38
views
Understanding Used Assembly: Why aren't authors specific about patch version?
GRCh38
gnomad
1000
assembly
genome
updated 1 hour ago by
GenoMax
129k • written 2 hours ago by
JourneyToAbyss
▴ 200
1
vote
1
reply
38
views
How to convert bed file to vcf?
vcf
bed
updated 2 hours ago by
Pierre Lindenbaum
154k • written 2 hours ago by
herh
• 0
0
votes
0
replies
21
views
METABOLOMICS DATA ANNOTATION
COMPOUND
METABOLOMICS
ANNOTATION
3 hours ago by
Rishabh Jha
• 0
0
votes
1
reply
47
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
updated 1 hour ago by
GenoMax
129k • written 5 hours ago by
NikhilP
▴ 20
0
votes
1
reply
56
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
CD
analysis
bioinformatic
Protocol
updated 2 hours ago by
barslmn
★ 1.5k • written 6 hours ago by
linnet.roque6
▴ 10
3
votes
9
replies
1.9k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 6 hours ago by
Pegasus
▴ 90 • written 3.6 years ago by
mnazir
▴ 10
0
votes
1
reply
92
views
BAM creation - vg surject vs vg mpmap output
mpmap
surject
vg
bam
updated 7 hours ago by
Rachel
• 0 • written 8 hours ago by
AshleeThomson
• 0
0
votes
0
replies
55
views
RRBS fastq - biased per base sequence content
fastqc
rrbs
8 hours ago by
mbk0asis
▴ 660
0
votes
0
replies
51
views
PRSice-2 using SNPs with extremely low P-value
PRSice-2
SNP
10 hours ago by
Apprentice
▴ 140
0
votes
0
replies
135
views
What are the existing proposals for how to approach genomic coordinates in a pangenome reference environment?
coordinates
pangenome
genomic
7 hours ago by
Vincent Laufer
★ 2.8k
0
votes
1
reply
147
views
Michigan Imputation Server - Local docker image
genotype
WGS
imputation
updated 11 hours ago by
Vincent Laufer
★ 2.8k • written 2 days ago by
batch_effect
• 0
0
votes
1
reply
111
views
Manhattan Plot with independent significant hits
Manhattan-plot
updated 11 hours ago by
Vincent Laufer
★ 2.8k • written 18 hours ago by
en_keser
• 0
0
votes
0
replies
71
views
Help with running ATAC using Encode pipeline
encode
ATAC-seq
13 hours ago by
Chris
▴ 100
0
votes
0
replies
65
views
Determining Cutoff for score in a bed file in ATAC-seq Data Analysis
bed
ATAC-seq
updated 13 hours ago by
Ram
39k • written 14 hours ago by
Mah
• 0
1
vote
3
replies
155
views
To call variants can I use my aligned WGS data as a reference genome
VCF
samtools
reference
genome
updated 14 hours ago by
GenoMax
129k • written 14 hours ago by
mls
• 0
0
votes
0
replies
71
views
snpEff error. No CDS checked
snpEff
gtf
WES
15 hours ago by
fifty_fifty
▴ 40
0
votes
0
replies
69
views
Tool to align metagenomic data to reference genome
tool
metagenomics
alignment
15 hours ago by
Maddie
• 0
0
votes
0
replies
66
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
15 hours ago by
rheab1230
▴ 140
1
vote
4
replies
168
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 13 hours ago by
Ram
39k • written 15 hours ago by
miguellarrazlopezdenovales
• 0
0
votes
2
replies
127
views
PacBio Pipeline and Tools for Variant Call
longread
pacbio
whatshap
pbmm2
1 hour ago by
Kiran
▴ 70
0
votes
0
replies
76
views
Count hexamer bias from pair end short read data
short
DESeq2
bias
read
hexamer
updated 16 hours ago by
rpolicastro
12k • written 17 hours ago by
Jjbox
▴ 40
0
votes
0
replies
54
views
Pore-C-Snakemake output files
contacts
16 hours ago by
oksana03fel
• 0
1
vote
0
replies
77
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
15 hours ago by
fr
▴ 200
1
vote
3
replies
218
views
Can any one suggest tools that generate "mind-maps" on concepts in biology/biotech?
Mind-maps
updated 16 hours ago by
Vincent Laufer
★ 2.8k • written 21 hours ago by
John Erik
• 0
3
votes
2
replies
104
views
Panther db Reference List
pantherdb
enrichment-tests
updated 15 hours ago by
Ram
39k • written 18 hours ago by
e.r.zakiev
▴ 50
0
votes
2
replies
133
views
Ambient RNA expression correction
scRNAseq
SoupX
Seurat
updated 16 hours ago by
rpolicastro
12k • written 18 hours ago by
Pac314
▴ 10
0
votes
1
reply
84
views
ABO alleles
ABO
variants
SNPs
alleles
updated 18 hours ago by
Raony Guimarães
★ 1.2k • written 19 hours ago by
Fernando
• 0
0
votes
1
reply
108
views
How to determine the exact version of hg38 if I have only the FASTA file
reference-genome
FASTA
updated 17 hours ago by
Ram
39k • written 19 hours ago by
mps
• 0
0
votes
2
replies
118
views
readGenericHeader() error message Limma
rna
limma
microarray
genomics
normalization
8 hours ago by
survive
• 0
1
vote
1
reply
97
views
mitochondrial genome, SRA PacBio sequencing.
Mitochondrial
PacBio
SRA
Mitogenome
updated 19 hours ago by
GenoMax
129k • written 20 hours ago by
hashim.rana11
• 0
2
votes
1
reply
133
views
sctransform on scRNA seq
seurat
updated 19 hours ago by
ATpoint
72k • written 23 hours ago by
friguiahlem8
▴ 10
0
votes
2
replies
93
views
Dot Plot using KEGG
KEGG
DotPlot
GO
updated 20 hours ago by
rpolicastro
12k • written 22 hours ago by
smanzano250800
• 0
13
votes
25
replies
3.0k
views
7 follow
VEP output has no gene names
alignment
sequencing
vep
updated 21 hours ago by
barslmn
★ 1.5k • written 4.8 years ago by
Gene_MMP8
▴ 230
0
votes
23
replies
333
views
gatk Hardfilter Error
hardfilter
updated 13 hours ago by
Michael
52k • written 1 day ago by
bestone
▴ 10
1
vote
1
reply
113
views
including samples for which group is unknown to help adjust for another variable
TCGA
design
RNA-Seq
deseq2
updated 6 hours ago by
Vincent Laufer
★ 2.8k • written 22 hours ago by
pilargmarch
▴ 80
0
votes
1
reply
86
views
Impute haplotypes (ImputePipelinePlugin) execution error - PHG
phg
updated 21 hours ago by
GenoMax
129k • written 1 day ago by
jrodrigu
• 0
3
votes
3
replies
148
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
updated 19 hours ago by
andres.firrincieli
3.3k • written 23 hours ago by
Sebastian Hesse
▴ 320
1
vote
7
replies
212
views
Docker Error while running nf-core/rnaseq pipeline
RNA-seq
nf-core
docker
updated 18 hours ago by
ATpoint
72k • written 1 day ago by
eesha28112001
• 0
2
votes
3
replies
141
views
What type of normalization did they use in this article?
normalization
TPM
r
updated 18 hours ago by
Ram
39k • written 1 day ago by
JACKY
▴ 100
1
vote
4
replies
157
views
MACS2 peak calling
MACS2
peak-calling
updated 18 hours ago by
seidel
11k • written 1 day ago by
Maurice
• 0
1
vote
1
reply
137
views
Which type of variant caller should I use in a WES normal cell line sample?
variant-caller
WES
updated 1 day ago by
ATpoint
72k • written 1 day ago by
bompipi95
▴ 120
5
votes
4
replies
161
views
Alignment of case vs. control from different origin
Alignment
RNAseq
updated 19 hours ago by
i.sudbery
17k • written 1 day ago by
sativus
• 0
110,388 results • Page
1 of 2208
Recent Votes
Answer: Understanding Used Assembly: Why aren't authors specific about patch version?
What ought to be the rate between methylated CpGs and CHX in RRBS ?
What ought to be the rate between methylated CpGs and CHX in RRBS ?
methylation coverage in the gene region
A: what's Validation stringency?
A: what's Validation stringency?
Comment: BioInformatics, Software
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Comment: ggsave() bug in ggplot2?
by
Medeea
• 0
>file("Figure1.jpg") A connection with description "Figure1.jpg" class "file" …
Comment: DEGseq for multiple samples
by
Basti
★ 1.5k
Your post is badly formatted, you should enhance the presentation. I do not understand your question because you created geneExpMatrix1 and…
Answer: Single Cell Rna Seq Using BD Rhapsody
by
GenoMax
129k
See answer here: https://www.biostars.org/p/9562237/#9562240 I don't think you can do this on Galaxy.
Comment: how to run FacetsSuite wrapper scripts on command line
by
GenoMax
129k
The [link in your original post][1] has this bit of help --snp-pileup-path <path to snp-pileup executable> So the path you provide ne…
Comment: ggsave() bug in ggplot2?
by
barslmn
★ 1.5k
Can you run the command `file Figure1.jpg` and post the output?
Comment: PacBio Pipeline and Tools for Variant Call
by
Kiran
▴ 70
Hi William , Thank you for the explanation, From VCF should i omit variants with `"/"` and keep ones with phased `"|"` for further annotati…
Comment: My kernel is killing the pairtools dedup script, how to prevent that?
by
GenoMax
129k
Keep an eye on memory usage. Even though you have 256G it is possible that the process is running out of memory or temp (/tmp) space. Try r…
Answer: Understanding Used Assembly: Why aren't authors specific about patch version?
by
GenoMax
129k
You may have seen explanation of the patches from GRC --> ([**LINK**][1]). > The fact that patch-version does matter for looking up varian…
Comment: how to run FacetsSuite wrapper scripts on command line
by
Dalal
• 0
I apologise for that. Unfortunately I am still left with the same error: > sh: 1: ~/mut_analysis/variant-calling/facets_cnv/: > Permission…
Comment: BioInformatics, Software
by
hashim.rana11
• 0
Thank you so much...
Comment: how to create correlation matrix R
by
satva72
• 0
great! thanks
Comment: BioInformatics, Software
by
barslmn
★ 1.5k
https://bio.tools/ is a great website indexing software used in bioinformatics.
Comment: BioInformatics, Software
by
Pierre Lindenbaum
154k
This is just too broad. what did you find so far ?
Answer: How to calculate kinship matrix table from vcf file
by
barslmn
★ 1.5k
You can use the vcftools relatedness2 module. Which implements the method describes in the paper: https://academic.oup.com/bioinformatics/a…
Answer: How to convert bed file to vcf?
by
Pierre Lindenbaum
154k
use AWK, change the header, body according to your needs... awk 'BEGIN {printf("##fileformat=VCFv4.2\n##INFO=<ID=END,Number=1,Type=I…
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