Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : today
all time
today
this week
this month
this year
113 results • Page
1 of 3
Sort: Rank
Rank
Views
Votes
Replies
2
votes
2
replies
15
views
How to extract haplotype data from phased bcf files
gwas
vcf
bcftools
wgs
phasing
just now by
Lynne-95
• 0
0
votes
1
reply
23
views
convert data frame with character column to data frame with integer column
r
updated 47 minutes ago by
Basti
★ 1.5k • written 1 hour ago by
atemedorri137798
• 0
0
votes
1
reply
64
views
DE genes across multiple scRNAseq clusters-are they significantly enriched?
Single-cell
updated 40 minutes ago by
ATpoint
72k • written 5 hours ago by
thaddeusknkl
• 0
0
votes
0
replies
33
views
how to call variants in haploid genome
human
haploid
genome
3 hours ago by
itsmesmb
• 0
4
votes
6
replies
1.4k
views
Why weblogo of biopython doesn't work?
Biopython
Weblogo
updated 6 hours ago by
minakshiboruahassam
• 0 • written 9 months ago by
Plus
▴ 20
0
votes
2
replies
211
views
Make a BedGraph file
BedGraph
RepeatMasker
BED
updated 6 hours ago by
rfran010
▴ 80 • written 3 days ago by
kirillkirilenko
▴ 10
0
votes
1
reply
75
views
The famous WGS dataset, Ashkenazi Trio?
wgs
dataset
updated 5 hours ago by
cmdcolin
★ 3.0k • written 6 hours ago by
herh
• 0
2
votes
3
replies
321
views
What is the best way to clean bulk RNA-seq data?
normalization
TPM
r
updated 6 hours ago by
rfran010
▴ 80 • written 3 days ago by
JACKY
▴ 100
1
vote
1
reply
140
views
Help with running ATAC using Encode pipeline
encode
ATAC-seq
updated 7 hours ago by
rfran010
▴ 80 • written 1 day ago by
Chris
▴ 100
10
votes
8
replies
372
views
7 follow
BioInformatics, Software
Learning
Software
updated 7 hours ago by
rfran010
▴ 80 • 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 7 hours ago by
Bryan
• 0 • written 3.8 years ago by
margab
▴ 10
0
votes
1
reply
53
views
RNASeq gene labeling and mRNA filter from bulkRNA data.
RNA-Seq
RSubreads
updated 2 hours ago by
ATpoint
72k • written 7 hours ago by
Yeeshouw
• 0
2
votes
1
reply
92
views
Optimum setting for local blastp for ~10K sequences
blast
blastp
hpc
updated 8 hours ago by
GenoMax
129k • written 11 hours ago by
sodiumnitrate
▴ 20
1
vote
0
replies
68
views
Integrating mRNA and microRNA analysis results
mRNA
microRNA
10 hours ago by
abba647
▴ 10
3
votes
4
replies
186
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 11 hours ago by
ATpoint
72k • written 12 hours ago by
bioinfo
▴ 80
0
votes
0
replies
70
views
Merge different vcf files
vcf
ref
merge
alleles
13 hours ago by
caique.manochio
• 0
11
votes
4
replies
242
views
how to sort a fasta file
fasta
updated 13 hours ago by
Pierre Lindenbaum
154k • written 21 hours ago by
Mohd
▴ 10
0
votes
4
replies
190
views
Identification of genes involved in my pathway
KEGG
keggGet
10 hours ago by
smanzano250800
• 0
4
votes
2
replies
149
views
How to detect specific genes in metagenomics data
metagenomics
genes
updated 13 hours ago by
Ram
39k • written 19 hours ago by
aziznasr1920
▴ 10
0
votes
0
replies
135
views
Job:
Senior Bioinformatics Research Scientistt/Bioinformatics Research Scientist-Epigenetics(USA, Memphis, TN, St. Jude Children's Research Hospital)
Tennessee
Hospital
Epigenetics
Memphis
11 hours ago by
xubeisi
▴ 30
7
votes
14
replies
437
views
ggsave() bug in ggplot2?
R
ggplot2
updated 15 hours ago by
Ram
39k • written 23 hours ago by
Medeea
▴ 10
1
vote
6
replies
227
views
How GATK pipeline called a homozygeous alternate allele (1/1) although one copy is supported by 0 reads ?
SNP
GATK
11 hours ago by
mohsamir2016
▴ 30
0
votes
6
replies
204
views
The inchworm process failed. Trinity running error.
inchworm
transcriptome
trinity
updated 17 hours ago by
GenoMax
129k • written 23 hours ago by
Marta
• 0
1
vote
1
reply
113
views
Combination of ROC CURVE
roccurve
R
AUC
updated 12 hours ago by
seidel
11k • written 18 hours ago by
Maria17
▴ 20
3
votes
2
replies
165
views
Understanding Used Assembly: Why aren't authors specific about patch version?
1000genomes
GRCh38
gnomad
assembly
freeze
updated 12 hours ago by
Jeremy Leipzig
21k • written 1 day ago by
JourneyToAbyss
▴ 210
0
votes
1
reply
85
views
what is the difference between FindVariableFeatures and FindAllMarkers?
Seurat
single-cell
FindVariableFeatures
FindAllMarkers
RNA-Seq
updated 19 hours ago by
rpolicastro
12k • written 19 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
3
replies
200
views
Impute haplotypes (ImputePipelinePlugin) execution error - PHG
phg
updated 13 hours ago by
lcj34
▴ 230 • written 1 day ago by
jrodrigu
• 0
1
vote
0
replies
68
views
Considering gaps in calculating conservation score from MSA
multiple
alignment
sequence
conservation
python
19 hours ago by
Jonathan Lefebre
▴ 50
6
votes
7
replies
318
views
including samples for which group is unknown to help adjust for another variable
TCGA
design
RNA-Seq
deseq2
updated 16 hours ago by
Vincent Laufer
★ 2.9k • written 1 day ago by
pilargmarch
▴ 100
0
votes
1
reply
88
views
Data is not displaying in DATABASE......error is not showing in IDE
SERVER
DATABASE
PHP
updated 20 hours ago by
GenoMax
129k • written 21 hours ago by
Souvik
• 0
4
votes
6
replies
228
views
Single Cell Rna Seq Using BD Rhapsody
Rhapsody
BD
updated 18 hours ago by
Ram
39k • written 23 hours ago by
abbas.waseem.gcu
▴ 20
0
votes
3
replies
146
views
DEGseq for multiple samples
DEGseq
DEG
updated 18 hours ago by
Ram
39k • written 1 day ago by
ALOUSH ALI
• 0
4
votes
2
replies
146
views
How to calculate kinship matrix table from vcf file
variants
haplotyping
kinship
heatmap
updated 17 hours ago by
chrchang523
10k • written 1 day ago by
rj.rezwan
• 0
0
votes
0
replies
62
views
Metabolomics Data Annotation
annotation
metabolomics
camera
updated 17 hours ago by
Ram
39k • written 1 day ago by
Rishabh Jha
• 0
1
vote
3
replies
156
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
updated 18 hours ago by
GenoMax
129k • written 1 day ago by
NikhilP
▴ 20
2
votes
2
replies
144
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
CD
analysis
bioinformatic
Protocol
updated 15 hours ago by
Dr William Klubinski
▴ 80 • written 1 day ago by
linnet.roque6
▴ 10
3
votes
12
replies
2.1k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 12 hours ago by
Pegasus
▴ 90 • written 3.6 years ago by
mnazir
▴ 10
0
votes
2
replies
168
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
11 hours ago by
rheab1230
▴ 140
2
votes
4
replies
264
views
PacBio Pipeline and Tools for Variant Call
longread
pacbio
whatshap
pbmm2
3 hours ago by
Kiran
▴ 80
1
vote
4
replies
164
views
Dot Plot using KEGG
KEGG
DotPlot
GO
21 hours ago by
smanzano250800
• 0
0
votes
3
replies
170
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
21 hours ago by
Mohd
▴ 10
1
vote
6
replies
514
views
Counting intronic reads in bulk RNA-seq
rna-seq
updated 9 hours ago by
swbarnes2
13k • written 6 days ago by
John Ma
▴ 300
0
votes
11
replies
535
views
how to run FacetsSuite wrapper scripts on command line
facets-suite
facets
updated 20 hours ago by
GenoMax
129k • written 8 days ago by
Dalal
• 0
4
votes
5
replies
571
views
how to design a guide RNA
genomics
updated 7 hours ago by
rfran010
▴ 80 • written 13 days ago by
Bioinfo
• 0
1
vote
4
replies
440
views
best annotation approach for peaks
chipseeker
R
chippeakanno
updated 8 hours ago by
rfran010
▴ 80 • written 17 days ago by
Chironex
▴ 40
2
votes
3
replies
433
views
ATAC peak-calling: same peak ID across multiple experimental conditions?
Genrich
ATAC
updated 8 hours ago by
rfran010
▴ 80 • written 20 days ago by
weimichelles
• 0
10
votes
15
replies
1.0k
views
Forum:
How should reference genome fasta files be distributed by UCSC?
reference-genome
fasta
freeze
ucsc-genome-browser
updated 12 hours ago by
Jeremy Leipzig
21k • written 3 months ago by
Maximilian Haeussler
★ 1.5k
3
votes
5
replies
1.7k
views
Remap GRCh38.p13 to GRCh38
haplotype
bed
genome
freeze
map
updated 12 hours ago by
Jeremy Leipzig
21k • written 2.2 years ago by
schmau
▴ 10
5
votes
7
replies
1.7k
views
How to prevent reduce from being performed in GRanges during setdiff
blunt-end
genomicranges
setdiff
updated 11 hours ago by
hossiny
• 0 • written 2.3 years ago by
Bosberg
▴ 50
2
votes
5
replies
1.6k
views
NarrowPeak format -Peak field
ChIP-Seq
dnase-seq
bed
updated 17 hours ago by
ATpoint
72k • written 2.7 years ago by
kimkes25
▴ 50
113 results • Page
1 of 3
Recent Votes
Comment: My kernel is killing the pairtools dedup script, how to prevent that?
Comment: ggsave() bug in ggplot2?
Comment: BioInformatics, Software
Comment: Single Cell Rna Seq Using BD Rhapsody
Comment: DP meaning in VCF files
Answer: Help with running ATAC using Encode pipeline
Comment: sorting BAM file
Recent Locations •
All
China,
just now
United States,
1 minute ago
Turkey,
1 minute ago
Russia,
1 minute ago
Japan,
2 minutes ago
United States,
3 minutes ago
South Korea,
4 minutes ago
Recent Awards •
All
Popular Question
to
mari.johnson
• 0
Commentator
to
barslmn
★ 1.6k
Popular Question
to
MobiusT
▴ 10
Popular Question
to
akshay_ware
▴ 30
Popular Question
to
Daniel
▴ 30
Popular Question
to
eb13
▴ 20
Scholar
to
seidel
11k
Recent Replies
Answer: How to extract haplotype data from phased bcf files
by
Pierre Lindenbaum
154k
use %TGT (translated genotype) $ bcftools query -f '[%CHROM %POS %TGT\n]'
Comment: convert data frame with character column to data frame with integer column
by
Basti
★ 1.5k
You would better give an example with values because we don't know what is in each variable so we cannot give you a precise code, but seems…
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
by
ATpoint
72k
This information is annotated in GTF files. You can get them for almost every annotated species from Ensembl. There is a column `gene_bioty…
Answer: DE genes across multiple scRNAseq clusters-are they significantly enriched?
by
ATpoint
72k
First of all, with thousands of DEGs you might want to choose a DE framework that allows testing against a fold change threshold, such as `…
Comment: PacBio Pipeline and Tools for Variant Call
by
Kiran
▴ 80
Thanks a lot William, I am Clear now
Comment: The famous WGS dataset, Ashkenazi Trio?
by
cmdcolin
★ 3.0k
what is valuable information to you
Answer: Why weblogo of biopython doesn't work?
by
minakshiboruahassam
• 0
The weblogo3 application is giving same file even if u run the scripts separately on python standalone or whatever. The weblogo command is …
Answer: Make a BedGraph file
by
rfran010
▴ 80
I would suggest bedtools makewindows to generate your 3,000bp bins then bedtools coverage to generate fraction of repeats over your windows…
Answer: What is the best way to clean bulk RNA-seq data?
by
rfran010
▴ 80
Honestly, I am a fan of visualizing to select a threshold since these can depend on the specific experiment. I would even just run standard…
Answer: Help with running ATAC using Encode pipeline
by
rfran010
▴ 80
Read all instructions carefully Specifically, this info is under the "Input JSON file specification" section with details in the followin…
Answer: BioInformatics, Software
by
rfran010
▴ 80
There have been some good suggestions, but it seems like you may be asking one of two questions, either (1) how to do bioinformatics? or (2…
Answer: Genome assembly statistical tools
by
Bryan
• 0
I'll follow up what a few others have mentioned, but I like stats.sh within the BBTools package for raw assembly stats. I'll then polish my…
Comment: how to design a guide RNA
by
rfran010
▴ 80
I agree this is very basic CRISPR mechanism and you'd be better off reading sites that could explain better than me. However, there is a lo…
Comment: ATAC peak-calling: same peak ID across multiple experimental conditions?
by
rfran010
▴ 80
You want to use the MACS2 score columns? You can retain these with bedtools option `-c` . This will retain the score columns from any merge…
Comment: best annotation approach for peaks
by
rfran010
▴ 80
The number of regions annotated as "Promoters" is the same regardless of TSS length? You can add this argument to annotatePeak (for mouse M…
Traffic: 2462 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6