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758 results • Page
1 of 16
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0
votes
1
reply
6
views
All combinations of two columns R
alleles
R
reorder
columns
updated just now by
Basti
★ 1.5k • written 7 minutes ago by
Fernando
• 0
0
votes
0
replies
7
views
Processing WES VCF for case control GWAS analysis
GWAS
PLINK
21 minutes ago by
sonsunjirachote
• 0
2
votes
2
replies
23
views
How to extract haplotype data from phased bcf files
gwas
vcf
bcftools
wgs
phasing
31 minutes ago by
Lynne-95
• 0
0
votes
1
reply
34
views
convert data frame with character column to data frame with integer column
r
updated 1 hour ago by
Basti
★ 1.5k • written 1 hour ago by
atemedorri137798
• 0
0
votes
1
reply
71
views
DE genes across multiple scRNAseq clusters-are they significantly enriched?
Single-cell
updated 1 hour ago by
ATpoint
72k • written 5 hours ago by
thaddeusknkl
• 0
0
votes
0
replies
36
views
how to call variants in haploid genome
human
haploid
genome
4 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
216
views
Make a BedGraph file
BedGraph
RepeatMasker
BED
updated 7 hours ago by
rfran010
▴ 90 • written 3 days ago by
kirillkirilenko
▴ 10
0
votes
1
reply
77
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
327
views
What is the best way to clean bulk RNA-seq data?
normalization
TPM
r
updated 7 hours ago by
rfran010
▴ 90 • written 3 days ago by
JACKY
▴ 100
2
votes
1
reply
143
views
Help with running ATAC using Encode pipeline
encode
ATAC-seq
updated 7 hours ago by
rfran010
▴ 90 • written 1 day ago by
Chris
▴ 100
10
votes
8
replies
379
views
7 follow
BioInformatics, Software
Learning
Software
updated 7 hours ago by
rfran010
▴ 90 • 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
60
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
95
views
Optimum setting for local blastp for ~10K sequences
blast
blastp
hpc
updated 9 hours ago by
GenoMax
129k • written 11 hours ago by
sodiumnitrate
▴ 20
1
vote
0
replies
70
views
Integrating mRNA and microRNA analysis results
mRNA
microRNA
10 hours ago by
abba647
▴ 10
3
votes
4
replies
187
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 12 hours ago by
ATpoint
72k • written 13 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
243
views
how to sort a fasta file
fasta
updated 13 hours ago by
Pierre Lindenbaum
154k • written 22 hours ago by
Mohd
▴ 10
0
votes
4
replies
193
views
Identification of genes involved in my pathway
KEGG
keggGet
11 hours ago by
smanzano250800
• 0
4
votes
2
replies
149
views
How to detect specific genes in metagenomics data
metagenomics
genes
updated 14 hours ago by
Ram
39k • written 20 hours ago by
aziznasr1920
▴ 10
0
votes
0
replies
137
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
439
views
ggsave() bug in ggplot2?
R
ggplot2
updated 15 hours ago by
Ram
39k • written 1 day ago by
Medeea
▴ 10
1
vote
6
replies
229
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
207
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
113
views
Combination of ROC CURVE
roccurve
R
AUC
updated 13 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 20 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
3
replies
200
views
Impute haplotypes (ImputePipelinePlugin) execution error - PHG
phg
updated 14 hours ago by
lcj34
▴ 230 • written 1 day ago by
jrodrigu
• 0
1
vote
0
replies
69
views
Considering gaps in calculating conservation score from MSA
multiple
alignment
sequence
conservation
python
20 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 17 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 22 hours ago by
Souvik
• 0
4
votes
6
replies
231
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
1
vote
1
reply
93
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
62
views
Metabolomics Data Annotation
annotation
metabolomics
camera
updated 18 hours ago by
Ram
39k • written 1 day ago by
Rishabh Jha
• 0
1
vote
3
replies
158
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
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
1
reply
134
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
92
views
RRBS fastq - biased per base sequence content
fastqc
rrbs
1 day ago by
mbk0asis
▴ 660
0
votes
0
replies
84
views
PRSice-2 using SNPs with extremely low P-value
PRSice-2
SNP
1 day ago by
Apprentice
▴ 140
0
votes
0
replies
275
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
181
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
145
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
92
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
197
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
101
views
snpEff error. No CDS checked
snpEff
gtf
WES
1 day ago by
fifty_fifty
▴ 40
0
votes
0
replies
100
views
Tool to align metagenomic data to reference genome
tool
metagenomics
alignment
1 day ago by
Maddie
• 0
758 results • Page
1 of 16
Recent Votes
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?
Comment: BioInformatics, Software
Comment: Single Cell Rna Seq Using BD Rhapsody
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Recent Replies
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
▴ 90
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
▴ 90
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
▴ 90
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
▴ 90
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
▴ 90
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…
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