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110,414 results • Page
1 of 2209
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0
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0
replies
1
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hardfilter error
bam
recall
just now by
bestone
▴ 10
0
votes
1
reply
26
views
Creating a local version of Clustered NR database
diamond
blast
clustered
ncbi
nr
updated just now by
GenoMax
129k • written 2 hours ago by
Wilford203
• 0
0
votes
0
replies
15
views
Gene expression analysis with missing data
RNAseq
updated 17 minutes ago by
4galaxy77
2.7k • written 31 minutes ago by
Sara
▴ 220
0
votes
1
reply
144
views
News:
7th Berlin Summer School in NGS Data Analysis (September 4-8 in Berlin)
DNA-Seq
Calling
Variant
RNA-Seq
Transcriptomics
32 minutes ago by
David Langenberger
9.9k
0
votes
0
replies
8
views
cnetplot enrichment graph to cytoscape
clusterprofiler
cnetplot
enrichplot
40 minutes ago by
Omics data mining
▴ 220
0
votes
2
replies
21
views
how to Construct a Newick tree file from five large fasta files
treefile
alignment
sequence
Newick
Multiple
18 minutes ago by
gunala.nikhil
• 0
0
votes
0
replies
15
views
How to extract the surrogate variables from DNA methlation Data
sva
array
limma
methylation
updated 31 minutes ago by
GenoMax
129k • written 58 minutes ago by
Dablax
• 0
0
votes
1
reply
24
views
Reads with highest MAPQ values from SAM files are showing mismatches to reference sequence and IGV classified them as supplementary reads
minimap
Nanopore
IGV
updated 5 minutes ago by
GenoMax
129k • written 1 hour ago by
Mohd
▴ 10
0
votes
2
replies
31
views
bcftools "--filter-logic" flag, what + means?
bcftools
vcf
updated 1 hour ago by
Pierre Lindenbaum
154k • written 2 hours ago by
Eugene A
▴ 170
0
votes
5
replies
96
views
All combinations of two columns R
alleles
R
reorder
columns
updated 1 hour ago by
Matthias Zepper
3.7k • written 3 hours ago by
Fernando
• 0
0
votes
0
replies
11
views
Stratified sample assignment for analysis
design
experimental
stratification
1 hour ago by
fr
▴ 200
0
votes
0
replies
6
views
Convert tree into bifurcation table
Tree
Newick
ASR
Mutation
1 hour ago by
Alexandre
• 0
0
votes
1
reply
69
views
how to call variants in haploid genome
human
haploid
genome
updated 2 hours ago by
raphael.B
▴ 360 • written 7 hours ago by
itsmesmb
• 0
0
votes
0
replies
35
views
Processing WES VCF for case control GWAS analysis
GWAS
PLINK
2 hours ago by
sonsunjirachote
• 0
2
votes
2
replies
71
views
How to extract haplotype data from phased bcf files
gwas
vcf
bcftools
wgs
phasing
3 hours ago by
Lynne-95
• 0
0
votes
1
reply
74
views
convert data frame with character column to data frame with integer column
r
updated 4 hours ago by
Basti
★ 1.5k • written 4 hours ago by
atemedorri137798
• 0
0
votes
1
reply
92
views
DE genes across multiple scRNAseq clusters-are they significantly enriched?
Single-cell
updated 4 hours ago by
ATpoint
72k • written 8 hours ago by
thaddeusknkl
• 0
4
votes
6
replies
1.4k
views
Why weblogo of biopython doesn't work?
Biopython
Weblogo
updated 9 hours ago by
minakshiboruahassam
• 0 • written 9 months ago by
Plus
▴ 20
0
votes
2
replies
224
views
Make a BedGraph file
BedGraph
RepeatMasker
BED
updated 10 hours ago by
rfran010
▴ 100 • written 3 days ago by
kirillkirilenko
▴ 10
744
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
102
views
The famous WGS dataset, Ashkenazi Trio?
wgs
dataset
updated 8 hours ago by
cmdcolin
★ 3.0k • written 10 hours ago by
herh
• 0
2
votes
3
replies
339
views
What is the best way to clean bulk RNA-seq data?
normalization
TPM
r
updated 10 hours ago by
rfran010
▴ 100 • written 3 days ago by
JACKY
▴ 100
2
votes
1
reply
151
views
Help with running ATAC using Encode pipeline
encode
ATAC-seq
updated 10 hours ago by
rfran010
▴ 100 • written 1 day ago by
Chris
▴ 100
11
votes
8
replies
401
views
7 follow
BioInformatics, Software
Learning
Software
updated 10 hours ago by
rfran010
▴ 100 • written 1 day ago by
hashim.rana11
▴ 20
10
votes
8
replies
8.2k
views
9 follow
Genome assembly statistical tools
statistics
tools
Assembly
updated 11 hours ago by
Bryan
• 0 • written 3.8 years ago by
margab
▴ 10
0
votes
1
reply
77
views
RNASeq gene labeling and mRNA filter from bulkRNA data.
RNA-Seq
RSubreads
updated 5 hours ago by
ATpoint
72k • written 11 hours ago by
Yeeshouw
• 0
2
votes
1
reply
105
views
Optimum setting for local blastp for ~10K sequences
blast
blastp
hpc
updated 12 hours ago by
GenoMax
129k • written 14 hours ago by
sodiumnitrate
▴ 20
1
vote
0
replies
78
views
Integrating mRNA and microRNA analysis results
mRNA
microRNA
13 hours ago by
abba647
▴ 10
3
votes
4
replies
198
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 15 hours ago by
ATpoint
72k • written 16 hours ago by
bioinfo
▴ 80
0
votes
0
replies
78
views
Merge different vcf files
vcf
ref
merge
alleles
16 hours ago by
caique.manochio
• 0
11
votes
4
replies
254
views
how to sort a fasta file
fasta
updated 17 hours ago by
Pierre Lindenbaum
154k • written 1 day ago by
Mohd
▴ 10
0
votes
4
replies
201
views
Identification of genes involved in my pathway
KEGG
keggGet
14 hours ago by
smanzano250800
• 0
4
votes
2
replies
158
views
How to detect specific genes in metagenomics data
metagenomics
genes
updated 17 hours ago by
Ram
39k • written 23 hours ago by
aziznasr1920
▴ 10
0
votes
0
replies
153
views
Job:
Senior Bioinformatics Research Scientistt/Bioinformatics Research Scientist-Epigenetics(USA, Memphis, TN, St. Jude Children's Research Hospital)
Tennessee
Hospital
Epigenetics
Memphis
14 hours ago by
xubeisi
▴ 30
7
votes
14
replies
455
views
ggsave() bug in ggplot2?
R
ggplot2
updated 18 hours ago by
Ram
39k • written 1 day ago by
Medeea
▴ 10
1
vote
6
replies
238
views
How GATK pipeline called a homozygeous alternate allele (1/1) although one copy is supported by 0 reads ?
SNP
GATK
14 hours ago by
mohsamir2016
▴ 30
0
votes
8
replies
231
views
The inchworm process failed. Trinity running error.
inchworm
transcriptome
trinity
updated 29 minutes ago by
GenoMax
129k • written 1 day ago by
Marta
• 0
1
vote
1
reply
118
views
Combination of ROC CURVE
roccurve
R
AUC
updated 16 hours ago by
seidel
11k • written 21 hours ago by
Maria17
▴ 20
3
votes
2
replies
171
views
Understanding Used Assembly: Why aren't authors specific about patch version?
1000genomes
GRCh38
gnomad
assembly
freeze
updated 15 hours ago by
Jeremy Leipzig
21k • written 1 day ago by
JourneyToAbyss
▴ 210
0
votes
1
reply
90
views
what is the difference between FindVariableFeatures and FindAllMarkers?
Seurat
single-cell
FindVariableFeatures
FindAllMarkers
RNA-Seq
updated 23 hours ago by
rpolicastro
12k • written 23 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
4
replies
216
views
Impute haplotypes (ImputePipelinePlugin) execution error - PHG
phg
1 hour ago by
jrodrigu
• 0
1
vote
0
replies
74
views
Considering gaps in calculating conservation score from MSA
multiple
alignment
sequence
conservation
python
23 hours ago by
Jonathan Lefebre
▴ 50
6
votes
7
replies
327
views
including samples for which group is unknown to help adjust for another variable
TCGA
design
RNA-Seq
deseq2
updated 20 hours ago by
Vincent Laufer
★ 2.9k • written 1 day ago by
pilargmarch
▴ 100
0
votes
1
reply
97
views
Data is not displaying in DATABASE......error is not showing in IDE
SERVER
DATABASE
PHP
updated 23 hours ago by
GenoMax
129k • written 1 day ago by
Souvik
• 0
4
votes
6
replies
244
views
Single Cell Rna Seq Using BD Rhapsody
Rhapsody
BD
updated 21 hours ago by
Ram
39k • written 1 day ago by
abbas.waseem.gcu
▴ 20
0
votes
3
replies
155
views
DEGseq for multiple samples
DEGseq
DEG
updated 22 hours ago by
Ram
39k • written 1 day ago by
ALOUSH ALI
• 0
4
votes
2
replies
152
views
How to calculate kinship matrix table from vcf file
variants
haplotyping
kinship
heatmap
updated 20 hours ago by
chrchang523
10k • written 1 day ago by
rj.rezwan
• 0
1
vote
1
reply
100
views
How to convert bed file to vcf?
vcf
bed
updated 1 day ago by
Pierre Lindenbaum
154k • written 1 day ago by
herh
• 0
0
votes
0
replies
69
views
Metabolomics Data Annotation
annotation
metabolomics
camera
updated 21 hours ago by
Ram
39k • written 1 day ago by
Rishabh Jha
• 0
1
vote
3
replies
170
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
updated 22 hours ago by
GenoMax
129k • written 1 day ago by
NikhilP
▴ 20
110,414 results • Page
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Comment: making metadata file for differential gene expression analysis
Comment: Filter VCF file for variant alleles
Nanopore tutorial for beginners
Comment: The famous WGS dataset, Ashkenazi Trio?
Answer: BioInformatics, Software
Answer: Help with running ATAC using Encode pipeline
Answer: How to extract haplotype data from phased bcf files
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Answer: Creating a local version of Clustered NR database
by
GenoMax
129k
Clustering `nr` is done using `mmseqs2` as noted [**here**][1] and copied below. Be ready to have gobs of hardware available to do this. …
Comment: Reads with highest MAPQ values from SAM files are showing mismatches to referenc
by
GenoMax
129k
With long nanopore reads you are going to get alignments that will have "errors" since that is partly due to characteristic of how nanopore…
Comment: how to Construct a Newick tree file from five large fasta files
by
gunala.nikhil
• 0
I have 30 MB of each five fasta files verticilium species genomes , actually I'm working on augustus for genome annotation of those speci…
Answer: 7th Berlin Summer School in NGS Data Analysis (September 4-8 in Berlin)
by
David Langenberger
9.9k
There are already 2/3 of the seats gone. Register today and secure your place!
Comment: The inchworm process failed. Trinity running error.
by
GenoMax
129k
The initial `ERROR` is simply a warning so that is hopefully not the problem. What do you see when you run `java --version`? > died with r…
Comment: The inchworm process failed. Trinity running error.
by
Marta
• 0
With a sample, the error occurs in the previous step. This is the error I get with the flag --verbose *******************************…
Comment: how to Construct a Newick tree file from five large fasta files
by
Joe
21k
1. What have you tried? 2. You need to tell us WAY more about what data you have (how large is large? is each of the 5 a single sequence?…
Comment: bcftools "--filter-logic" flag, what + means?
by
Pierre Lindenbaum
154k
When you merge 3 records, if one has filter PASS and other has filter FOO, and the third has filter BAR setting `--filter-logic x` will …
Comment: Impute haplotypes (ImputePipelinePlugin) execution error - PHG
by
jrodrigu
• 0
Sure. The command is: singularity exec -B $PWD:/phg/ /ei/software/testing/phg/1.4/phg.img /tassel-5-standalone/run_pipeline.pl -debug …
Answer: bcftools "--filter-logic" flag, what + means?
by
raphael.B
▴ 360
When you merge 2 records, if one has filter `PASS` and other has filter `FOO`, setting `--filter-logic x` will return you a record with fil…
Answer: All combinations of two columns R
by
Matthias Zepper
3.7k
Like others, I am lost what you wish to achieve. If you are really talking about regular genomic positions and intervals / overlaps etc., h…
Comment: All combinations of two columns R
by
Fernando
• 0
The expected output would be to obtein a list of dataframes of all possible combinations of df1 column 1 and column 2 and at least one comb…
Comment: All combinations of two columns R
by
Basti
★ 1.5k
What would be your expected output in the example you gave ?
Comment: All combinations of two columns R
by
Fernando
• 0
For being honest, I do not know where to start with this. This is a valid example: This would be the test df with unordered columns: `df…
Answer: how to call variants in haploid genome
by
raphael.B
▴ 360
Hello, you can do this using GATK Haplotype Caller using the [--sample-ploidy](https://gatk.broadinstitute.org/hc/en-us/articles/3600372256…
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