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110,401 results • Page
1 of 2209
Sort: Rank
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Votes
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0
votes
0
replies
8
views
how to call variants in haploid genome
human
haploid
genome
26 minutes ago by
itsmesmb
• 0
0
votes
0
replies
16
views
DE genes across multiple scRNAseq clusters-are they significantly enriched?
Single-cell
1 hour ago by
thaddeusknkl
• 0
4
votes
6
replies
1.4k
views
Why weblogo of biopython doesn't work?
Biopython
Weblogo
updated 2 hours ago by
minakshiboruahassam
• 0 • written 9 months ago by
Plus
▴ 20
0
votes
2
replies
197
views
Make a BedGraph file
BedGraph
RepeatMasker
BED
updated 3 hours ago by
rfran010
▴ 80 • written 2 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
0
votes
1
reply
39
views
The famous WGS dataset, Ashkenazi Trio?
wgs
dataset
updated 1 hour ago by
cmdcolin
★ 3.0k • written 2 hours ago by
herh
• 0
2
votes
3
replies
304
views
What is the best way to clean bulk RNA-seq data?
normalization
TPM
r
updated 3 hours ago by
rfran010
▴ 80 • written 3 days ago by
JACKY
▴ 100
1
vote
1
reply
125
views
Help with running ATAC using Encode pipeline
encode
ATAC-seq
updated 3 hours ago by
rfran010
▴ 80 • written 1 day ago by
Chris
▴ 100
9
votes
8
replies
345
views
7 follow
BioInformatics, Software
Learning
Software
updated 3 hours ago by
rfran010
▴ 80 • written 20 hours ago by
hashim.rana11
▴ 20
10
votes
8
replies
8.2k
views
9 follow
Genome assembly statistical tools
statistics
tools
Assembly
updated 3 hours ago by
Bryan
• 0 • written 3.8 years ago by
margab
▴ 10
0
votes
0
replies
30
views
RNASeq gene labeling and mRNA filter from bulkRNA data.
RNA-Seq
RSubreads
3 hours ago by
Yeeshouw
• 0
2
votes
1
reply
78
views
Optimum setting for local blastp for ~10K sequences
blast
blastp
hpc
updated 5 hours ago by
GenoMax
129k • written 7 hours ago by
sodiumnitrate
▴ 20
1
vote
0
replies
56
views
Integrating mRNA and microRNA analysis results
mRNA
microRNA
6 hours ago by
abba647
▴ 10
3
votes
4
replies
170
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 8 hours ago by
ATpoint
72k • written 9 hours ago by
bioinfo
▴ 80
0
votes
0
replies
56
views
Merge different vcf files
vcf
ref
merge
alleles
9 hours ago by
caique.manochio
• 0
11
votes
4
replies
232
views
how to sort a fasta file
fasta
updated 9 hours ago by
Pierre Lindenbaum
154k • written 18 hours ago by
Mohd
▴ 10
0
votes
4
replies
171
views
Identification of genes involved in my pathway
KEGG
keggGet
7 hours ago by
smanzano250800
• 0
4
votes
2
replies
141
views
How to detect specific genes in metagenomics data
metagenomics
genes
updated 10 hours ago by
Ram
39k • written 16 hours ago by
aziznasr1920
▴ 10
0
votes
0
replies
108
views
Job:
Senior Bioinformatics Research Scientistt/Bioinformatics Research Scientist-Epigenetics(USA, Memphis, TN, St. Jude Children's Research Hospital)
Tennessee
Hospital
Epigenetics
Memphis
7 hours ago by
xubeisi
▴ 30
6
votes
14
replies
422
views
ggsave() bug in ggplot2?
R
ggplot2
updated 11 hours ago by
Ram
39k • written 20 hours ago by
Medeea
▴ 10
1
vote
6
replies
207
views
How GATK pipeline called a homozygeous alternate allele (1/1) although one copy is supported by 0 reads ?
SNP
GATK
7 hours ago by
mohsamir2016
▴ 30
0
votes
6
replies
196
views
The inchworm process failed. Trinity running error.
inchworm
transcriptome
trinity
updated 14 hours ago by
GenoMax
129k • written 20 hours ago by
Marta
• 0
1
vote
1
reply
105
views
Combination of ROC CURVE
roccurve
R
AUC
updated 9 hours ago by
seidel
11k • written 14 hours ago by
Maria17
▴ 20
3
votes
2
replies
158
views
Understanding Used Assembly: Why aren't authors specific about patch version?
1000genomes
GRCh38
gnomad
assembly
freeze
updated 8 hours ago by
Jeremy Leipzig
21k • written 20 hours ago by
JourneyToAbyss
▴ 210
0
votes
1
reply
78
views
what is the difference between FindVariableFeatures and FindAllMarkers?
Seurat
single-cell
FindVariableFeatures
FindAllMarkers
RNA-Seq
updated 15 hours ago by
rpolicastro
12k • written 16 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
3
replies
191
views
Impute haplotypes (ImputePipelinePlugin) execution error - PHG
phg
updated 10 hours ago by
lcj34
▴ 230 • written 1 day ago by
jrodrigu
• 0
1
vote
0
replies
61
views
Considering gaps in calculating conservation score from MSA
multiple
alignment
sequence
conservation
python
16 hours ago by
Jonathan Lefebre
▴ 50
6
votes
7
replies
308
views
including samples for which group is unknown to help adjust for another variable
TCGA
design
RNA-Seq
deseq2
updated 13 hours ago by
Vincent Laufer
★ 2.9k • written 1 day ago by
pilargmarch
▴ 100
0
votes
1
reply
79
views
Data is not displaying in DATABASE......error is not showing in IDE
SERVER
DATABASE
PHP
updated 16 hours ago by
GenoMax
129k • written 18 hours ago by
Souvik
• 0
3
votes
6
replies
209
views
Single Cell Rna Seq Using BD Rhapsody
Rhapsody
BD
updated 14 hours ago by
Ram
39k • written 19 hours ago by
abbas.waseem.gcu
▴ 20
0
votes
3
replies
140
views
DEGseq for multiple samples
DEGseq
DEG
updated 14 hours ago by
Ram
39k • written 20 hours ago by
ALOUSH ALI
• 0
4
votes
2
replies
140
views
How to calculate kinship matrix table from vcf file
variants
haplotyping
kinship
heatmap
updated 13 hours ago by
chrchang523
10k • written 21 hours ago by
rj.rezwan
• 0
1
vote
1
reply
83
views
How to convert bed file to vcf?
vcf
bed
updated 21 hours ago by
Pierre Lindenbaum
154k • written 21 hours ago by
herh
• 0
0
votes
0
replies
57
views
Metabolomics Data Annotation
annotation
metabolomics
camera
updated 14 hours ago by
Ram
39k • written 21 hours ago by
Rishabh Jha
• 0
0
votes
3
replies
146
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
updated 15 hours ago by
GenoMax
129k • written 23 hours ago by
NikhilP
▴ 20
2
votes
2
replies
138
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
CD
analysis
bioinformatic
Protocol
updated 11 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 8 hours ago by
Pegasus
▴ 90 • written 3.6 years ago by
mnazir
▴ 10
0
votes
1
reply
129
views
BAM creation - vg surject vs vg mpmap output
mpmap
surject
vg
bam
updated 1 day ago by
Rachel
• 0 • written 1 day ago by
AshleeThomson
• 0
0
votes
0
replies
86
views
RRBS fastq - biased per base sequence content
fastqc
rrbs
1 day ago by
mbk0asis
▴ 660
0
votes
0
replies
79
views
PRSice-2 using SNPs with extremely low P-value
PRSice-2
SNP
1 day ago by
Apprentice
▴ 140
0
votes
0
replies
253
views
What are the existing proposals for how to approach genomic coordinates in a pangenome reference environment?
coordinates
pangenome
genomic
1 day ago by
Vincent Laufer
★ 2.9k
0
votes
1
reply
176
views
Michigan Imputation Server - Local docker image
genotype
WGS
imputation
updated 1 day ago by
Vincent Laufer
★ 2.9k • written 3 days ago by
batch_effect
• 0
0
votes
1
reply
139
views
Manhattan Plot with independent significant hits
Manhattan-plot
updated 1 day ago by
Vincent Laufer
★ 2.9k • written 1 day ago by
en_keser
• 0
0
votes
0
replies
87
views
Determining Cutoff for score in a bed file in ATAC-seq Data Analysis
bed
ATAC-seq
updated 1 day ago by
Ram
39k • written 1 day ago by
Mah
• 0
1
vote
3
replies
191
views
To call variants can I use my aligned WGS data as a reference genome
VCF
samtools
reference
genome
updated 1 day ago by
GenoMax
129k • written 1 day ago by
mls
• 0
0
votes
0
replies
96
views
snpEff error. No CDS checked
snpEff
gtf
WES
1 day ago by
fifty_fifty
▴ 40
0
votes
0
replies
94
views
Tool to align metagenomic data to reference genome
tool
metagenomics
alignment
1 day ago by
Maddie
• 0
0
votes
2
replies
158
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
8 hours ago by
rheab1230
▴ 140
1
vote
4
replies
200
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 1 day ago by
Ram
39k • written 1 day ago by
miguellarrazlopezdenovales
• 0
2
votes
4
replies
241
views
PacBio Pipeline and Tools for Variant Call
longread
pacbio
whatshap
pbmm2
16 minutes ago by
Kiran
▴ 80
110,401 results • Page
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Recent Votes
Answer: Help with running ATAC using Encode pipeline
Comment: sorting BAM file
Comment: Create customized gene annotation file
Answer: MACS2 peak calling
Answer: How to determine the exact version of hg38 if I have only the FASTA file
PacBio Pipeline and Tools for Variant Call
Answer: how to sort a fasta file
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Recent Replies
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…
Answer: Optimum setting for local blastp for ~10K sequences
by
GenoMax
129k
It is possible that NCBI keeps the entire `nr` indexes in memory and searches against that so there is no I/O involved. NCBI now also uses …
Comment: Counting intronic reads in bulk RNA-seq
by
swbarnes2
13k
10x does give you a big flashing warning telling you what the new default is, and tells you how to redo it without that if it's not what yo…
Comment: Identification of genes involved in my pathway
by
smanzano250800
• 0
Thank you, but it doesn´t work. I´ll try GeneSCF again.
Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
by
mohsamir2016
▴ 30
Organism: gallus gallus Genome version used: GRCg6a Chr and Position: NC_006113.5, 24618 Ref allele: A Alt allele: G Genotype: 1/1 (G/G) …
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