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 : this year
all time
today
this week
this month
this year
1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
1
reply
19
views
Random dataset and DESeq2
DESeq2
updated 28 minutes ago by
LChart
2.6k • written 40 minutes ago by
Saleh
• 0
0
votes
0
replies
8
views
Differential protein expression analysis
R
proteomic
statistics
1 hour ago by
Ribo
▴ 40
0
votes
1
reply
14
views
(ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now ...
bowtie2
align_stats
trinity
updated 13 minutes ago by
GenoMax
129k • written 1 hour ago by
eimanpharmacist
▴ 20
0
votes
0
replies
42
views
What are recommended parameters for the local protein alignment ?
protein
alignment
4 hours ago by
Alexander
▴ 70
0
votes
0
replies
48
views
microsatellite, SSR, using Galaxy
Galaxy
SSR
using
microsatellite
10 hours ago by
m.esmaeilpour
▴ 10
0
votes
0
replies
57
views
decoupleR & Transcription Factory Activity Inference: pvalue or padj?
pvalue
padj
decoupleR
15 hours ago by
OST
▴ 10
2
votes
3
replies
195
views
Low mapping percentage
mapping
STAR
RNAseq
1 hour ago by
Sib
▴ 40
0
votes
0
replies
88
views
Visualization App for RNASeq Differential Expression and Enrichment Analysis
differential
visualization
RNASeq
analysis
expression
enrichment
23 hours ago by
Mark
• 0
0
votes
0
replies
77
views
calculate p value and associated z score for snp-gene pair
snp
association
gene
pvalue
1 day ago by
rheab1230
▴ 140
0
votes
0
replies
80
views
busco id description
OrthoDB
BUSCO
updated 1 day ago by
Ram
39k • written 1 day ago by
hembrom.angelina
• 0
0
votes
5
replies
266
views
how to Construct a Newick tree file from five large fasta files
tree
Newick
alignment
updated 23 hours ago by
Joe
21k • written 1 day ago by
gunala.nikhil
• 0
0
votes
0
replies
89
views
NMDS plotting issue
NMDS
metagenomic
1 day ago by
arshad1292
▴ 90
0
votes
1
reply
112
views
featurecounts not working on mirbase annotation file
usegalaxy
miRNA-seq
updated 23 hours ago by
GenoMax
129k • written 1 day ago by
demoraesdiogo2017
▴ 90
0
votes
0
replies
78
views
IGV insertions
insertions
IGV
1 day ago by
christoph.schubart
• 0
1
vote
0
replies
86
views
Bayesian network for biological data using bnlearn
bnlearn
RNA-seq
bayesian-network
updated 1 day ago by
Ram
39k • written 1 day ago by
priyankamehta.1811
▴ 10
0
votes
0
replies
76
views
jellyfish options
kmer
jellyfish
1 day ago by
Tele
• 0
0
votes
3
replies
132
views
hardfilter error
bam
recall
1 day ago by
bestone
▴ 10
0
votes
0
replies
69
views
cnetplot enrichment graph to cytoscape
clusterprofiler
cnetplot
enrichplot
1 day ago by
Omics data mining
▴ 220
0
votes
0
replies
76
views
How to extract the surrogate variables from DNA methlation Data
sva
array
limma
methylation
updated 1 day ago by
GenoMax
129k • written 1 day ago by
Dablax
• 0
1
vote
1
reply
291
views
Reads with highest MAPQ values from SAM files are showing mismatches to reference sequence and IGV classified them as supplementary reads
minimap
Nanopore
IGV
updated 1 day ago by
GenoMax
129k • written 1 day ago by
Mohd
▴ 20
0
votes
0
replies
71
views
Stratified sample assignment for analysis
experimental-design
stratification
updated 1 day ago by
Ram
39k • written 1 day ago by
fr
▴ 200
0
votes
0
replies
66
views
Convert tree into bifurcation table
Tree
Newick
ASR
Mutation
1 day ago by
Alexandre
• 0
0
votes
1
reply
118
views
Processing WES VCF for case control GWAS analysis
GWAS
PLINK
updated 1 day ago by
raphael.B
▴ 360 • written 1 day ago by
sonsunjirachote
• 0
0
votes
4
replies
251
views
convert data frame with character column to data frame with integer column
r
23 hours ago by
atemedorri137798
• 0
4
votes
6
replies
1.5k
views
Why weblogo of biopython doesn't work?
Biopython
Weblogo
updated 1 day ago by
minakshiboruahassam
• 0 • written 9 months ago by
Plus
▴ 20
1
vote
2
replies
174
views
The famous WGS dataset, Ashkenazi Trio?
wgs
dataset
updated 1 day ago by
thadjudkins2
• 0 • written 1 day ago by
herh
• 0
0
votes
1
reply
131
views
RNASeq gene labeling and mRNA filter from bulkRNA data.
RNA-Seq
RSubreads
updated 1 day ago by
ATpoint
72k • written 1 day ago by
Yeeshouw
• 0
1
vote
0
replies
126
views
Integrating mRNA and microRNA analysis results
mRNA
microRNA
1 day ago by
abba647
▴ 10
4
votes
4
replies
254
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 1 day ago by
ATpoint
72k • written 1 day ago by
bioinfo
▴ 80
0
votes
1
reply
141
views
Merge different vcf files
vcf
updated 1 day ago by
Ram
39k • written 2 days ago by
caique.manochio
• 0
0
votes
4
replies
247
views
Identification of genes involved in my pathway
KEGG
keggGet
1 day ago by
smanzano250800
• 0
0
votes
8
replies
303
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 1 day ago by
seidel
11k • written 2 days ago by
Maria17
▴ 20
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
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
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 1 day ago by
Pegasus
▴ 90 • written 3.7 years ago by
mnazir
▴ 10
0
votes
0
replies
101
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
0
replies
102
views
Determining Cutoff for score in a bed file in ATAC-seq Data Analysis
bed
ATAC-seq
updated 2 days ago by
Ram
39k • written 2 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 2 days ago by
GenoMax
129k • written 2 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
1 day ago by
rheab1230
▴ 140
2
votes
4
replies
227
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 2 days ago by
Ram
39k • written 3 days ago by
miguellarrazlopezdenovales
• 0
0
votes
0
replies
80
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
1,000 results • Page
1 of 20
Recent Votes
A: Single end or paired end for variant calling
Comment: Single end or paired end for variant calling
Comment: how to look for interactions between different chromosomes
Bioinformatics data integration
Answer: Hiplot: a simple and user-friendly visualization platform for scientific data
Multiomics data preprocessing
Comment: Low mapping percentage
Recent Locations •
All
Turkey,
1 minute ago
United States,
5 minutes ago
Germany,
6 minutes ago
Italy,
8 minutes ago
Romania,
19 minutes ago
Denmark,
19 minutes ago
Nigeria,
23 minutes ago
Recent Awards •
All
Popular Question
to
Siavash Salek Ardestani
▴ 20
Popular Question
to
Nai
▴ 50
Popular Question
to
Arindam Ghosh
▴ 500
Commentator
to
SmallChess
▴ 630
Popular Question
to
OST
▴ 10
Popular Question
to
carlopecoraro2
★ 2.3k
Teacher
to
Pierre Lindenbaum
154k
Recent Replies
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…
Comment: Help with running ATAC using Encode pipeline
by
Chris
▴ 100
Thank you for the instruction! I see the beside json file we also have input file which I am confused. Because we have already defined the …
Comment: Comparing loci across catalogs
by
rycro_c
• 0
Hi @Austin, Did you ever figure this out?
Comment: Low mapping percentage
by
Dave Carlson
★ 1.3k
I've been faced with similar issues in the past. Both option 1 and 2 seem useful. You can also treat your data as accidental metagenomic …
Comment: How to sort gff3 according to chromosome order?
by
Pierre Lindenbaum
154k
-s, --stable stabilize sort by disabling last-resort comparison
Comment: Low mapping percentage
by
GenoMax
129k
If you do have contamination (either from rRNA of same species or from true contaminant(s)) there is not much you can do about that at this…
Comment: Optimum setting for local blastp for ~10K sequences
by
GenoMax
129k
> Running the same sequence on the blast web server took 10 seconds Don't try to compare anything local with NCBI's web blast infrastruct…
Comment: how to Construct a Newick tree file from five large fasta files
by
Joe
21k
Yes, I know - but that doesn't answer the question. **What *kind* of phylogenetic tree?**
Traffic: 1043 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