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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
4
views
Creating a local version of Clustered NR database
diamond
blast
clustered
ncbi
nr
3 minutes ago by
Wilford203
• 0
0
votes
0
replies
4
views
bcftools "--filter-logic" flag, what + means?
bcftools
vcf
10 minutes ago by
Eugene A
▴ 170
0
votes
1
reply
48
views
how to call variants in haploid genome
human
haploid
genome
updated 33 minutes ago by
raphael.B
▴ 360 • written 5 hours ago by
itsmesmb
• 0
0
votes
4
replies
41
views
All combinations of two columns R
alleles
R
reorder
columns
4 minutes ago by
Fernando
• 0
0
votes
0
replies
15
views
Processing WES VCF for case control GWAS analysis
GWAS
PLINK
30 minutes ago by
sonsunjirachote
• 0
2
votes
2
replies
34
views
How to extract haplotype data from phased bcf files
gwas
vcf
bcftools
wgs
phasing
1 hour ago by
Lynne-95
• 0
0
votes
1
reply
49
views
convert data frame with character column to data frame with integer column
r
updated 2 hours ago by
Basti
★ 1.5k • written 2 hours ago by
atemedorri137798
• 0
0
votes
1
reply
77
views
DE genes across multiple scRNAseq clusters-are they significantly enriched?
Single-cell
updated 2 hours ago by
ATpoint
72k • written 6 hours ago by
thaddeusknkl
• 0
4
votes
6
replies
1.4k
views
Why weblogo of biopython doesn't work?
Biopython
Weblogo
updated 7 hours ago by
minakshiboruahassam
• 0 • written 9 months ago by
Plus
▴ 20
0
votes
2
replies
217
views
Make a BedGraph file
BedGraph
RepeatMasker
BED
updated 7 hours ago by
rfran010
▴ 100 • written 3 days ago by
kirillkirilenko
▴ 10
1
vote
1
reply
83
views
The famous WGS dataset, Ashkenazi Trio?
wgs
dataset
updated 6 hours ago by
cmdcolin
★ 3.0k • written 7 hours ago by
herh
• 0
2
votes
3
replies
328
views
What is the best way to clean bulk RNA-seq data?
normalization
TPM
r
updated 8 hours ago by
rfran010
▴ 100 • written 3 days ago by
JACKY
▴ 100
2
votes
1
reply
146
views
Help with running ATAC using Encode pipeline
encode
ATAC-seq
updated 8 hours ago by
rfran010
▴ 100 • written 1 day ago by
Chris
▴ 100
11
votes
8
replies
386
views
7 follow
BioInformatics, Software
Learning
Software
updated 8 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 8 hours ago by
Bryan
• 0 • written 3.8 years ago by
margab
▴ 10
0
votes
1
reply
66
views
RNASeq gene labeling and mRNA filter from bulkRNA data.
RNA-Seq
RSubreads
updated 3 hours ago by
ATpoint
72k • written 8 hours ago by
Yeeshouw
• 0
2
votes
1
reply
96
views
Optimum setting for local blastp for ~10K sequences
blast
blastp
hpc
updated 10 hours ago by
GenoMax
129k • written 12 hours ago by
sodiumnitrate
▴ 20
1
vote
0
replies
71
views
Integrating mRNA and microRNA analysis results
mRNA
microRNA
11 hours ago by
abba647
▴ 10
3
votes
4
replies
189
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 13 hours ago by
ATpoint
72k • written 14 hours ago by
bioinfo
▴ 80
0
votes
0
replies
72
views
Merge different vcf files
vcf
ref
merge
alleles
14 hours ago by
caique.manochio
• 0
11
votes
4
replies
245
views
how to sort a fasta file
fasta
updated 14 hours ago by
Pierre Lindenbaum
154k • written 23 hours ago by
Mohd
▴ 10
0
votes
4
replies
196
views
Identification of genes involved in my pathway
KEGG
keggGet
12 hours ago by
smanzano250800
• 0
4
votes
2
replies
152
views
How to detect specific genes in metagenomics data
metagenomics
genes
updated 15 hours ago by
Ram
39k • written 21 hours ago by
aziznasr1920
▴ 10
0
votes
0
replies
140
views
Job:
Senior Bioinformatics Research Scientistt/Bioinformatics Research Scientist-Epigenetics(USA, Memphis, TN, St. Jude Children's Research Hospital)
Tennessee
Hospital
Epigenetics
Memphis
12 hours ago by
xubeisi
▴ 30
7
votes
14
replies
443
views
ggsave() bug in ggplot2?
R
ggplot2
updated 16 hours ago by
Ram
39k • written 1 day ago by
Medeea
▴ 10
1
vote
6
replies
230
views
How GATK pipeline called a homozygeous alternate allele (1/1) although one copy is supported by 0 reads ?
SNP
GATK
12 hours ago by
mohsamir2016
▴ 30
0
votes
6
replies
210
views
The inchworm process failed. Trinity running error.
inchworm
transcriptome
trinity
updated 18 hours ago by
GenoMax
129k • written 1 day ago by
Marta
• 0
1
vote
1
reply
114
views
Combination of ROC CURVE
roccurve
R
AUC
updated 14 hours ago by
seidel
11k • written 19 hours ago by
Maria17
▴ 20
3
votes
2
replies
166
views
Understanding Used Assembly: Why aren't authors specific about patch version?
1000genomes
GRCh38
gnomad
assembly
freeze
updated 13 hours ago by
Jeremy Leipzig
21k • written 1 day ago by
JourneyToAbyss
▴ 210
0
votes
1
reply
87
views
what is the difference between FindVariableFeatures and FindAllMarkers?
Seurat
single-cell
FindVariableFeatures
FindAllMarkers
RNA-Seq
updated 20 hours ago by
rpolicastro
12k • written 21 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
3
replies
201
views
Impute haplotypes (ImputePipelinePlugin) execution error - PHG
phg
updated 15 hours ago by
lcj34
▴ 230 • written 1 day ago by
jrodrigu
• 0
1
vote
0
replies
70
views
Considering gaps in calculating conservation score from MSA
multiple
alignment
sequence
conservation
python
21 hours ago by
Jonathan Lefebre
▴ 50
6
votes
7
replies
319
views
including samples for which group is unknown to help adjust for another variable
TCGA
design
RNA-Seq
deseq2
updated 18 hours ago by
Vincent Laufer
★ 2.9k • written 1 day ago by
pilargmarch
▴ 100
0
votes
1
reply
89
views
Data is not displaying in DATABASE......error is not showing in IDE
SERVER
DATABASE
PHP
updated 21 hours ago by
GenoMax
129k • written 23 hours ago by
Souvik
• 0
4
votes
6
replies
234
views
Single Cell Rna Seq Using BD Rhapsody
Rhapsody
BD
updated 19 hours ago by
Ram
39k • written 1 day ago by
abbas.waseem.gcu
▴ 20
0
votes
3
replies
149
views
DEGseq for multiple samples
DEGseq
DEG
updated 19 hours ago by
Ram
39k • written 1 day ago by
ALOUSH ALI
• 0
4
votes
2
replies
147
views
How to calculate kinship matrix table from vcf file
variants
haplotyping
kinship
heatmap
updated 18 hours ago by
chrchang523
10k • written 1 day ago by
rj.rezwan
• 0
1
vote
1
reply
95
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
63
views
Metabolomics Data Annotation
annotation
metabolomics
camera
updated 19 hours ago by
Ram
39k • written 1 day ago by
Rishabh Jha
• 0
1
vote
3
replies
160
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
updated 19 hours ago by
GenoMax
129k • written 1 day ago by
NikhilP
▴ 20
2
votes
2
replies
146
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
CD
analysis
bioinformatic
Protocol
updated 16 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 13 hours ago by
Pegasus
▴ 90 • written 3.6 years ago by
mnazir
▴ 10
0
votes
1
reply
135
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
93
views
RRBS fastq - biased per base sequence content
fastqc
rrbs
1 day ago by
mbk0asis
▴ 660
0
votes
0
replies
85
views
PRSice-2 using SNPs with extremely low P-value
PRSice-2
SNP
1 day ago by
Apprentice
▴ 140
0
votes
0
replies
284
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
182
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
147
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
93
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
199
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
1,000 results • Page
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Recent Votes
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
Answer: How to extract haplotype data from phased bcf files
Comment: My kernel is killing the pairtools dedup script, how to prevent that?
Comment: ggsave() bug in ggplot2?
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Recent Replies
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…
Comment: Difference between Allele frequency spectrum and Joint allele frequency spectrum
by
jena
▴ 250
> Where is the 21th comparison coming from? The bins are from 0 to 20, so you are probably missing the zero bin of no alleles (minor, deri…
Comment: All combinations of two columns R
by
Basti
★ 1.5k
Where are you stuck ? You need to give a reproducible example if you want a precise answer
Comment: How to extract haplotype data from phased bcf files
by
Lynne-95
• 0
Thanks that worked perfectly!
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
▴ 100
I would suggest bedtools makewindows to generate your 3,000bp bins then bedtools coverage to generate fraction of repeats over your windows…
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