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673 results • Page
2 of 14
Sort: Rank
Rank
Views
Votes
Replies
2
votes
3
replies
304
views
Help with running ATAC using Encode pipeline
encode
ATAC-seq
updated 3 hours ago by
rfran010
▴ 100 • written 3 days ago by
Chris
▴ 100
11
votes
8
replies
491
views
7 follow
BioInformatics, Software
Learning
Software
updated 1 day ago by
rfran010
▴ 100 • written 2 days ago by
hashim.rana11
▴ 20
10
votes
8
replies
8.3k
views
9 follow
Genome assembly statistical tools
statistics
tools
Assembly
updated 1 day ago by
Bryan
• 0 • written 3.8 years ago by
margab
▴ 10
4
votes
3
replies
262
views
Optimum setting for local blastp for ~10K sequences
blast
blastp
hpc
updated 1 day ago by
GenoMax
129k • written 2 days ago by
sodiumnitrate
▴ 20
1
vote
0
replies
126
views
Integrating mRNA and microRNA analysis results
mRNA
microRNA
2 days ago by
abba647
▴ 10
4
votes
4
replies
255
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 2 days ago by
ATpoint
72k • written 2 days ago by
bioinfo
▴ 80
0
votes
1
reply
143
views
Merge different vcf files
vcf
updated 1 day ago by
Ram
39k • written 2 days ago by
caique.manochio
• 0
11
votes
4
replies
311
views
how to sort a fasta file
fasta
updated 2 days ago by
Pierre Lindenbaum
154k • written 2 days ago by
Mohd
▴ 20
0
votes
4
replies
249
views
Identification of genes involved in my pathway
KEGG
keggGet
2 days ago by
smanzano250800
• 0
4
votes
2
replies
186
views
How to detect specific genes in metagenomics data
metagenomics
genes
updated 2 days ago by
Ram
39k • written 2 days ago by
aziznasr1920
▴ 10
0
votes
0
replies
214
views
Job:
Senior Bioinformatics Research Scientistt/Bioinformatics Research Scientist-Epigenetics(USA, Memphis, TN, St. Jude Children's Research Hospital)
Tennessee
Hospital
Epigenetics
Memphis
2 days ago by
xubeisi
▴ 30
7
votes
14
replies
501
views
ggsave() bug in ggplot2?
R
ggplot2
updated 2 days ago by
Ram
39k • written 2 days ago by
Medeea
▴ 10
1
vote
7
replies
292
views
How GATK pipeline called a homozygeous alternate allele (1/1) although one copy is supported by 0 reads ?
SNP
GATK
updated 1 day ago by
Ram
39k • written 2 days ago by
mohsamir2016
▴ 30
0
votes
8
replies
308
views
The inchworm process failed. Trinity running error.
inchworm
transcriptome
trinity
updated 1 day ago by
GenoMax
129k • written 2 days ago by
Marta
• 0
1
vote
1
reply
137
views
Combination of ROC CURVE
roccurve
R
AUC
updated 2 days ago by
seidel
11k • written 2 days ago by
Maria17
▴ 20
3
votes
2
replies
191
views
Understanding Used Assembly: Why aren't authors specific about patch version?
1000genomes
GRCh38
gnomad
assembly
freeze
updated 2 days ago by
Jeremy Leipzig
21k • written 2 days ago by
JourneyToAbyss
▴ 210
0
votes
1
reply
104
views
what is the difference between FindVariableFeatures and FindAllMarkers?
Seurat
single-cell
FindVariableFeatures
FindAllMarkers
RNA-Seq
updated 2 days ago by
rpolicastro
12k • written 2 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
5
replies
295
views
Impute haplotypes (ImputePipelinePlugin) execution error - PHG
phg
updated 1 day ago by
lcj34
▴ 230 • written 3 days ago by
jrodrigu
• 0
1
vote
0
replies
82
views
Considering gaps in calculating conservation score from MSA
multiple
alignment
sequence
conservation
python
2 days ago by
Jonathan Lefebre
▴ 50
6
votes
7
replies
349
views
including samples for which group is unknown to help adjust for another variable
TCGA
design
RNA-Seq
deseq2
updated 2 days ago by
Vincent Laufer
★ 2.9k • written 3 days ago by
pilargmarch
▴ 100
0
votes
1
reply
108
views
Data is not displaying in DATABASE......error is not showing in IDE
SERVER
DATABASE
PHP
updated 2 days ago by
GenoMax
129k • written 2 days ago by
Souvik
• 0
4
votes
6
replies
275
views
Single Cell Rna Seq Using BD Rhapsody
Rhapsody
BD
updated 2 days ago by
Ram
39k • written 2 days ago by
abbas.waseem.gcu
▴ 20
0
votes
3
replies
165
views
DEGseq for multiple samples
DEGseq
DEG
updated 2 days ago by
Ram
39k • written 2 days ago by
ALOUSH ALI
• 0
4
votes
2
replies
162
views
How to calculate kinship matrix table from vcf file
variants
haplotyping
kinship
heatmap
updated 2 days ago by
chrchang523
10k • written 2 days ago by
rj.rezwan
• 0
1
vote
1
reply
108
views
How to convert bed file to vcf?
vcf
bed
updated 2 days ago by
Pierre Lindenbaum
154k • written 2 days ago by
herh
• 0
0
votes
0
replies
73
views
Metabolomics Data Annotation
annotation
metabolomics
camera
updated 2 days ago by
Ram
39k • written 2 days ago by
Rishabh Jha
• 0
1
vote
3
replies
186
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
updated 2 days ago by
GenoMax
129k • written 2 days ago by
NikhilP
▴ 20
2
votes
2
replies
171
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
CD
analysis
bioinformatic
Protocol
updated 2 days ago by
Dr William Klubinski
▴ 80 • written 2 days 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 2 days ago by
Pegasus
▴ 90 • written 3.7 years ago by
mnazir
▴ 10
0
votes
1
reply
149
views
BAM creation - vg surject vs vg mpmap output
mpmap
surject
vg
bam
updated 2 days ago by
Rachel
• 0 • written 2 days ago by
AshleeThomson
• 0
0
votes
0
replies
102
views
RRBS fastq - biased per base sequence content
fastqc
rrbs
2 days ago by
mbk0asis
▴ 660
0
votes
0
replies
94
views
PRSice-2 using SNPs with extremely low P-value
PRSice-2
SNP
2 days ago by
Apprentice
▴ 140
0
votes
0
replies
298
views
What are the existing proposals for how to approach genomic coordinates in a pangenome reference environment?
coordinates
pangenome
genomic
2 days ago by
Vincent Laufer
★ 2.9k
0
votes
1
reply
191
views
Michigan Imputation Server - Local docker image
genotype
WGS
imputation
updated 3 days ago by
Vincent Laufer
★ 2.9k • written 4 days ago by
batch_effect
• 0
0
votes
1
reply
158
views
Manhattan Plot with independent significant hits
Manhattan-plot
updated 3 days ago by
Vincent Laufer
★ 2.9k • written 3 days ago by
en_keser
• 0
0
votes
0
replies
102
views
Determining Cutoff for score in a bed file in ATAC-seq Data Analysis
bed
ATAC-seq
updated 3 days ago by
Ram
39k • written 3 days ago by
Mah
• 0
1
vote
3
replies
213
views
To call variants can I use my aligned WGS data as a reference genome
VCF
samtools
reference
genome
updated 3 days ago by
GenoMax
129k • written 3 days ago by
mls
• 0
0
votes
0
replies
105
views
snpEff error. No CDS checked
snpEff
gtf
WES
3 days ago by
fifty_fifty
▴ 40
0
votes
0
replies
103
views
Tool to align metagenomic data to reference genome
tool
metagenomics
alignment
3 days ago by
Maddie
• 0
1
vote
2
replies
186
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
2 days ago by
rheab1230
▴ 140
2
votes
4
replies
227
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 3 days ago by
Ram
39k • written 3 days ago by
miguellarrazlopezdenovales
• 0
2
votes
4
replies
302
views
PacBio Pipeline and Tools for Variant Call
longread
pacbio
whatshap
pbmm2
1 day ago by
Kiran
▴ 80
0
votes
0
replies
99
views
Count hexamer bias from pair end short read data
short
DESeq2
bias
read
hexamer
updated 3 days ago by
rpolicastro
12k • written 3 days ago by
Jjbox
▴ 40
0
votes
0
replies
81
views
Pore-C-Snakemake output files
contacts
3 days ago by
oksana03fel
• 0
1
vote
0
replies
104
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
3 days ago by
fr
▴ 200
3
votes
3
replies
270
views
Can any one suggest tools that generate "mind-maps" on concepts in biology/biotech?
Mind-maps
updated 3 days ago by
Vincent Laufer
★ 2.9k • written 3 days ago by
John Erik
• 0
3
votes
2
replies
145
views
Panther db Reference List
pantherdb
enrichment-tests
updated 3 days ago by
Ram
39k • written 3 days ago by
e.r.zakiev
▴ 50
0
votes
2
replies
170
views
Ambient RNA expression correction
scRNAseq
SoupX
Seurat
updated 3 days ago by
rpolicastro
12k • written 3 days ago by
Pac314
▴ 10
0
votes
1
reply
120
views
ABO alleles
ABO
variants
SNPs
alleles
updated 3 days ago by
Raony Guimarães
★ 1.2k • written 3 days ago by
Fernando
• 0
1
vote
1
reply
144
views
How to determine the exact version of hg38 if I have only the FASTA file
reference-genome
FASTA
updated 3 days ago by
Ram
39k • written 3 days ago by
mps
• 0
673 results • Page
2 of 14
Recent Votes
Answer: I have one fasta file of a bacteria. Can i use to create a phylogenetic tree?
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
[Meta] Use of AI
Answer: Network cross-validation
Answer: Random dataset and DESeq2
A: Single end or paired end for variant calling
Comment: Single end or paired end for variant calling
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Comment: Is a human genome file with reference as NCBI37 the same as hg19?
by
a5864557
• 0
Note: I've also asked this [here][1] [1]: https://bioinformatics.stackexchange.com/questions/21101/is-a-human-genome-file-with-referenc…
Answer: [Meta] Use of AI
by
GenoMax
129k
As you indicate, AI in some form or other is here to stay and we can't avoid it in our lives and on biostars. Main issue I see is the vali…
Answer: RNASeq gene labeling and mRNA filter from bulkRNA data.
by
rfran010
▴ 100
featureCounts can extract this information and output a column for you during counting, presuming you input a GTF file. `extraAttributes …
Comment: What are recommended parameters for the local protein alignment ?
by
Alexander
▴ 70
Trying to do so ))
Comment: Help with running ATAC using Encode pipeline
by
rfran010
▴ 100
The "Input files" section is details on how you can specify your fastqs in the JSON. (You specify all pipeline parameters in the JSON.) Ess…
Comment: What are recommended parameters for the local protein alignment ?
by
Vincent Laufer
★ 2.9k
does this mean you understand pident now and are moving forward?
Answer: Random dataset and DESeq2
by
Vincent Laufer
★ 2.9k
@e38da452 Not only is this not surprising, it is the basis for an entire class of statistical techniques referred to as permutation bas…
Comment: (ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now
by
GenoMax
129k
> This generated multiple Trinity.fa files in the index folder Did the process complete successfully?
Comment: Random dataset and DESeq2
by
LChart
2.6k
I don't think you've given enough detail about your approach (what's the data? are you correcting for covariates? how did you shuffle? how …
Answer: Network cross-validation
by
LChart
2.6k
What do you mean by "robust" in this case? Which of the following is closest to what you want to estimate: (1) Would I get a similar res…
Comment: I have one fasta file of a bacteria. Can i use to create a phylogenetic tree?
by
Mustafa
• 0
Thank you so much ! will try them all !
Answer: I have one fasta file of a bacteria. Can i use to create a phylogenetic tree?
by
andres.firrincieli
3.3k
If the fasta file contains the genome sequence you can use the following: 1. GToTree (see example [here][1]) 2. [GTDB-tk][2] *de novo…
Comment: Low mapping percentage
by
Sib
▴ 40
Thank you for the reply @genomax . If there is not much I can do about the contamination at this stage, what is the benefit of knowing the…
Answer: integrate single cell RNA sequencing data
by
Hamid Ghaedi
2.9k
There are different approaches that you may choose to deal with batch correction. Harmony is one of those approaches that has been shown to…
Comment: What does canonical transcript mean in the context of VEP
by
Vincent Laufer
★ 2.9k
@curious - The only thing I have to add to @yokofakun 's precise answer is that, while you are considering and reading about Ensembl canoni…
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