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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
26
views
Network cross-validation
wgcna
RNASeq
Network
CV
2 hours ago by
Arindam Ghosh
▴ 500
0
votes
0
replies
18
views
microsatellite, SSR, using Galaxy
Galaxy
SSR
using
microsatellite
2 hours ago by
m.esmaeilpour
▴ 10
0
votes
0
replies
37
views
decoupleR & Transcription Factory Activity Inference: pvalue or padj?
pvalue
padj
decoupleR
8 hours ago by
OST
▴ 10
2
votes
3
replies
156
views
Low mapping percentage
mapping
STAR
RNAseq
1 hour ago by
Sib
▴ 40
0
votes
0
replies
69
views
Visualization App for RNASeq Differential Expression and Enrichment Analysis
differential
visualization
RNASeq
analysis
expression
enrichment
15 hours ago by
Mark
• 0
0
votes
0
replies
65
views
calculate p value and associated z score for snp-gene pair
snp
association
gene
pvalue
16 hours ago by
rheab1230
▴ 140
0
votes
0
replies
71
views
busco id description
OrthoDB
BUSCO
updated 19 hours ago by
Ram
39k • written 20 hours ago by
hembrom.angelina
• 0
0
votes
5
replies
244
views
how to Construct a Newick tree file from five large fasta files
tree
Newick
alignment
updated 15 hours ago by
Joe
21k • written 1 day ago by
gunala.nikhil
• 0
0
votes
0
replies
79
views
NMDS plotting issue
NMDS
metagenomic
21 hours ago by
arshad1292
▴ 90
0
votes
1
reply
97
views
featurecounts not working on mirbase annotation file
usegalaxy
miRNA-seq
updated 15 hours ago by
GenoMax
129k • written 21 hours ago by
demoraesdiogo2017
▴ 90
0
votes
0
replies
69
views
IGV insertions
insertions
IGV
22 hours ago by
christoph.schubart
• 0
1
vote
0
replies
76
views
Bayesian network for biological data using bnlearn
bnlearn
RNA-seq
bayesian-network
updated 18 hours ago by
Ram
39k • written 23 hours ago by
priyankamehta.1811
▴ 10
0
votes
0
replies
64
views
jellyfish options
kmer
jellyfish
23 hours ago by
Tele
• 0
0
votes
3
replies
120
views
hardfilter error
bam
recall
23 hours ago by
bestone
▴ 10
0
votes
0
replies
59
views
cnetplot enrichment graph to cytoscape
clusterprofiler
cnetplot
enrichplot
1 day ago by
Omics data mining
▴ 220
0
votes
0
replies
66
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
248
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
60
views
Stratified sample assignment for analysis
experimental-design
stratification
updated 18 hours ago by
Ram
39k • written 1 day ago by
fr
▴ 200
0
votes
0
replies
57
views
Convert tree into bifurcation table
Tree
Newick
ASR
Mutation
1 day ago by
Alexandre
• 0
0
votes
1
reply
107
views
Processing WES VCF for case control GWAS analysis
GWAS
PLINK
updated 23 hours ago by
raphael.B
▴ 360 • written 1 day ago by
sonsunjirachote
• 0
0
votes
4
replies
228
views
convert data frame with character column to data frame with integer column
r
15 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
163
views
The famous WGS dataset, Ashkenazi Trio?
wgs
dataset
updated 19 hours ago by
thadjudkins2
• 0 • written 1 day ago by
herh
• 0
0
votes
1
reply
119
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
119
views
Integrating mRNA and microRNA analysis results
mRNA
microRNA
1 day ago by
abba647
▴ 10
4
votes
4
replies
251
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 18 hours ago by
Ram
39k • written 1 day ago by
caique.manochio
• 0
0
votes
4
replies
244
views
Identification of genes involved in my pathway
KEGG
keggGet
1 day ago by
smanzano250800
• 0
0
votes
8
replies
291
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
136
views
Combination of ROC CURVE
roccurve
R
AUC
updated 1 day ago by
seidel
11k • written 1 day ago by
Maria17
▴ 20
1
vote
0
replies
82
views
Considering gaps in calculating conservation score from MSA
multiple
alignment
sequence
conservation
python
1 day ago by
Jonathan Lefebre
▴ 50
0
votes
3
replies
162
views
DEGseq for multiple samples
DEGseq
DEG
updated 1 day ago by
Ram
39k • written 2 days ago by
ALOUSH ALI
• 0
0
votes
0
replies
72
views
Metabolomics Data Annotation
annotation
metabolomics
camera
updated 1 day ago by
Ram
39k • written 2 days ago by
Rishabh Jha
• 0
1
vote
3
replies
180
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
updated 1 day ago by
GenoMax
129k • written 2 days ago by
NikhilP
▴ 20
2
votes
2
replies
168
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
CD
analysis
bioinformatic
Protocol
updated 1 day 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
100
views
RRBS fastq - biased per base sequence content
fastqc
rrbs
2 days ago by
mbk0asis
▴ 660
0
votes
0
replies
92
views
PRSice-2 using SNPs with extremely low P-value
PRSice-2
SNP
2 days ago by
Apprentice
▴ 140
0
votes
0
replies
296
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
100
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
209
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
103
views
snpEff error. No CDS checked
snpEff
gtf
WES
2 days ago by
fifty_fifty
▴ 40
0
votes
0
replies
101
views
Tool to align metagenomic data to reference genome
tool
metagenomics
alignment
2 days ago by
Maddie
• 0
0
votes
2
replies
180
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
1 day ago by
rheab1230
▴ 140
2
votes
4
replies
224
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 2 days ago by
Ram
39k • written 2 days ago by
miguellarrazlopezdenovales
• 0
0
votes
0
replies
78
views
Pore-C-Snakemake output files
contacts
2 days ago by
oksana03fel
• 0
1
vote
0
replies
102
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
2 days ago by
fr
▴ 200
0
votes
2
replies
166
views
Ambient RNA expression correction
scRNAseq
SoupX
Seurat
updated 2 days ago by
rpolicastro
12k • written 2 days ago by
Pac314
▴ 10
0
votes
2
replies
148
views
readGenericHeader() error message Limma
rna
limma
microarray
genomics
normalization
2 days ago by
survive
• 0
1
vote
1
reply
122
views
mitochondrial genome, SRA PacBio sequencing.
Mitochondrial
PacBio
SRA
Mitogenome
updated 2 days ago by
GenoMax
129k • written 2 days ago by
hashim.rana11
▴ 20
1,000 results • Page
1 of 20
Recent Votes
Comment: Low mapping percentage
Comment: Low mapping percentage
A: genomicranges outside sequence bounds
A: how can i download human ribosomal reference ?
Bayesian network for biological data using bnlearn
Comment: What does canonical transcript mean in the context of VEP
Answer: What does canonical transcript mean in the context of VEP
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Siavash Salek Ardestani
▴ 20
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▴ 50
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▴ 500
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carlopecoraro2
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Recent Replies
Comment: Low mapping percentage
by
Sib
▴ 40
Thank you for the reply. If there is not much I can do about the contamination at this stage, what is the benefit of knowing the source of…
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?**
Comment: Optimum setting for local blastp for ~10K sequences
by
sodiumnitrate
▴ 20
Thank you for the explanation! I managed to get diamond to work, but I'm having trouble getting it to run faster than blast. For a single t…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
by
GenoMax
129k
That is the question @Vincent answer poses since it seems to correspond to something different. You can also create an issue on https://gi…
Answer: How to sort gff3 according to chromosome order?
by
GenoMax
129k
Please use `AGAT`: https://agat.readthedocs.io/en/latest/topological-sorting-of-gff-features.html
Comment: convert data frame with character column to data frame with integer column
by
atemedorri137798
• 0
dear @Basti : As you said in order to clarify my issue I edit question box with give an example. I will be grateful if you take a look at …
Comment: How to sort gff3 according to chromosome order?
by
Ram
39k
Those are your options with the `sort` utility - you can either keep the existing order or re-order by coordinate. If you're looking for a …
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