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
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
89
views
SVA correction reduces ability to detect genes as differential expressed?
effects
RNAseq
expression
batch
SVA
gene
3 days ago by
MB
▴ 50
0
votes
7
replies
383
views
CoveragePlot in Signac from MACS2 Object
Signac
scATAC-seq
updated 3 days ago by
seidel
10k • written 3 days ago by
bioinformatics.girl
• 0
0
votes
1
reply
158
views
Remove duplicates in multifasta, where entries are paired
bash
python
updated 3 days ago by
dthorbur
▴ 260 • written 3 days ago by
SaltedPork
▴ 170
1
vote
2
replies
192
views
snakemake Unexpected keyword bam in rule definition
snakemake
1 day ago by
Aidand
• 0
0
votes
0
replies
84
views
Normalize Together Total RNA-SEQ vs Ampliseq protocols reads
RNA-seq
deseq2
ampliseq
ion-torrent
R
4 days ago by
Fernando
• 0
0
votes
0
replies
87
views
Combining mRNA and total RNA studies
RNA-Seq
bulk
updated 3 days ago by
Ram
37k • written 4 days ago by
aksh
• 0
0
votes
0
replies
78
views
Twist Exome Sequencing Data: Palindromic Tandem Insertion-Deletion
NGS
Artefact
Twist
Sequencing
Exome
4 days ago by
TraPS-VarI
• 0
0
votes
0
replies
140
views
Bootstrap in PhyML
phyml
bootstrap
4 days ago by
Jimpix
▴ 10
0
votes
0
replies
118
views
Cibersort phenotpe file to create signature matrix
deconvolution
cibersort
file
phenotype
4 days ago by
ce810b57
• 0
0
votes
0
replies
131
views
Enrichment map in python/ Pathway network by using python
interaction.
enrichment
network
pathway
analysis
4 days ago by
sonsunjirachote
• 0
0
votes
1
reply
186
views
How to analysis genomes with orthologs?
ortholog
genome
annotation
updated 4 days ago by
GenoMax
125k • written 4 days ago by
沛煒
• 0
0
votes
0
replies
120
views
Does the falcon input CLR reads need corrected by Canu?
Genome
assemble
4 days ago by
leeunfeng
• 0
0
votes
0
replies
104
views
CUT&RUN H3K27me3 normalization with spike-in
deepTools
4 days ago by
mohansri1
• 0
0
votes
0
replies
120
views
How to identify nodes in a network with a higher degree and higher edge variance?
network
variance
WGCNA
igraph
updated 4 days ago by
ATpoint
68k • written 4 days ago by
adR
▴ 100
0
votes
2
replies
203
views
Can you apply Base Score Recalibration in parallel?
wgs
updated 4 days ago by
LChart
1.8k • written 4 days ago by
optimistsso4co3
▴ 100
0
votes
3
replies
281
views
Change accession number to chromosome number in reference genome
fasta
chromosome
updated 3 days ago by
Ram
37k • written 4 days ago by
Tsigabu
• 0
0
votes
0
replies
94
views
Median depth across samples from multi-sample VCF
DP
bcftools
4 days ago by
alex.blakes
• 0
0
votes
5
replies
268
views
Add Information to Protein Fasta Headers
protein
fasta
functional-annotation
header
4 days ago by
ahmadjoyyia
▴ 10
3
votes
2
replies
178
views
WGCNA gene selection: gene significance or LASSO?
LASSO
WGCNA
updated 4 days ago by
rpolicastro
11k • written 4 days ago by
janinubinu
• 0
0
votes
0
replies
93
views
why count_matrix.csv generated by "prepDE.py3" showed unidentified IDs
Stringtie
RNA-seq
22 hours ago by
Pegasus
▴ 40
0
votes
3
replies
289
views
biological vs. technical definition of "insert size"
grinder
simulated-reads
shotgun-sequencing
updated 4 days ago by
ATpoint
68k • written 5 days ago by
sovrappensiero
▴ 50
0
votes
0
replies
88
views
Haloplex HS - should you remove duplicates?
deduplicate
Haloplex
duplicates
5 days ago by
amy__
▴ 50
0
votes
0
replies
92
views
Interpreting SnpEff output plots
NGS
Annotation
SnpEff
WGS
WES
5 days ago by
Alireza
▴ 20
0
votes
0
replies
81
views
Using DANPOS2 to determine nucleosome positions
MNase-seq
DANPOS
ENCODE
bigwig
5 days ago by
elisheva
▴ 120
0
votes
0
replies
89
views
How to determine the receptor and binding site of a protein transcribed from a gene
gene
5 days ago by
yoser4
▴ 10
0
votes
3
replies
181
views
blast engine error empty blast query vector
error
alignment
Blast
updated 5 days ago by
pbioinf
▴ 30 • written 5 days ago by
Sowmya Pulapet
▴ 10
0
votes
0
replies
99
views
WGCNA Error in moduleEigengenes: setting key from pcagrey to pcagrey_
wgcna
5 days ago by
瀚
• 0
0
votes
0
replies
103
views
Exon 1 coverage of ADAMTS2 gene
WGS
Coverage
5 days ago by
ramya
• 0
0
votes
0
replies
121
views
bcftools error: bcftools could not parse pval threshold loidly
bcftools
mpileup
5 days ago by
mut.patricia
▴ 20
0
votes
0
replies
144
views
How to show the correlation between the expression of one gene and all the cell miRNAs expression levels?
expression
miRNA
correlation
5 days ago by
Zahra
▴ 90
0
votes
2
replies
190
views
No variants found ( have problem in the handbook)
bcftools
handbook
variation_calling
igv
5 days ago by
quanyu
• 0
0
votes
0
replies
136
views
Anti-CRISPR and Cas protein interactions
crispr
anti-crispr
proteins
updated 5 days ago by
GenoMax
125k • written 5 days ago by
Moein
• 0
0
votes
0
replies
134
views
issues with amber_minimize.py failing to use CUDA within alphafold
linux
CUDA
amber
alphafold
5 days ago by
charlieclark1ee
▴ 10
1
vote
1
reply
170
views
tools that align sequences in mouse and human
r
updated 5 days ago by
dthorbur
▴ 260 • written 5 days ago by
Chironex
▴ 40
0
votes
0
replies
125
views
Database of Embryo-Lethal or Known Knockout Phenotype Genes in Rice
annotation
database
rice
gene
5 days ago by
sviatoslav.kendall
▴ 840
0
votes
0
replies
135
views
Application of the branch, site and branch-site models for detecting selection with codeml (PAML)
evolution
codeml
PAML
5 days ago by
Denis
▴ 260
0
votes
0
replies
119
views
How to normalize the counts when you are looking at 3'UTR?
RNA-Seq
bedtools
5 days ago by
barrypraveen
▴ 100
1
vote
3
replies
231
views
Strand-specific in HT-Seq
HT-Seq
Strand-specific
5 days ago by
ibq.enriquepola
• 0
1
vote
1
reply
182
views
Visualize variants and percentage of variants from one sample of Amplicon Seq data?
Amplicon
PCR
RNAseq
GATK
BWA
updated 4 days ago by
cmdcolin
★ 2.8k • written 5 days ago by
Saran
▴ 20
0
votes
2
replies
170
views
Where can I get the ICB datasets in this website?
data
r
ICB
updated 5 days ago by
GenoMax
125k • written 6 days ago by
JACKY
▴ 70
0
votes
0
replies
92
views
Alternatives to DendroCypher tool for large trees labeling
selection
PAML
codeml
pressure
6 days ago by
Denis
▴ 260
1
vote
3
replies
222
views
How to correctly use bedtools merge?
bedtools
updated 6 days ago by
Ram
37k • written 6 days ago by
Amisha
• 0
0
votes
4
replies
675
views
dbSNP and indels
VCF
6 days ago by
wonde2000
• 0
0
votes
1
reply
159
views
How to choose --mind value for plink SNPs filtering
SNPs
mind
plink
filter
updated 19 hours ago by
Fabio Marroni
★ 2.9k • written 6 days ago by
anithanagaraj93
• 0
1
vote
2
replies
221
views
Speciation of insecta using NGS technology
speciation
NGS
18S
insecta
5 days ago by
dante
• 0
0
votes
5
replies
301
views
Unable to install clusterProfiler on Mac M1
install
M1
Mac
clusterProfiler
updated 6 days ago by
GenoMax
125k • written 6 days ago by
Wang Cong
▴ 10
0
votes
0
replies
109
views
Error: line 1 did not have 7 elements. --Putting bismark extractor files into methimpute
RNA-seq
updated 6 days ago by
Ram
37k • written 6 days ago by
sam
• 0
0
votes
0
replies
105
views
Lastz align sequence to self in blocks of 1kb
LASTZ
chromosome
self-align
6 days ago by
polag01
▴ 10
1
vote
1
reply
200
views
Find ASVs for Non-Microbial Data
Amplicon
ASV
PCR
BWA
VCF
updated 5 days ago by
andres.firrincieli
3.1k • written 6 days ago by
Saran
▴ 20
0
votes
0
replies
113
views
pathwaycommons SPARQL endpoint down?
pathwaycommons
6 days ago by
mk
▴ 270
1,000 results • Page
2 of 20
Recent Votes
Answer: How can I convert this pairwise format to fasta?
Answer: How can I convert this pairwise format to fasta?
Piping bowtie2 output directly into BAM
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
Comment: RNA Editing data from RNA-seq
Comment: RNA Editing data from RNA-seq
Recent Locations •
All
Cambridge, MA,
just now
Colombia,
just now
Canada,
1 minute ago
Finland,
2 minutes ago
United Kingdom,
3 minutes ago
Whitefish, MT,
3 minutes ago
France,
3 minutes ago
Recent Awards •
All
Popular Question
to
Matteo Schiavinato
★ 3.6k
Popular Question
to
Barry Digby
★ 1.1k
Popular Question
to
Lee Katz
★ 3.1k
Scholar
to
GenoMax
125k
Scholar
to
Nicolas Rosewick
10k
Popular Question
to
Papyrus
★ 2.3k
Guru
to
Adrian Altenhoff
★ 1.0k
Recent Replies
Answer: What type of database does gnomAD use?
by
Jeremy Leipzig
21k
If you primarily want a variant warehouse that supports genomic region and sample queries at biobank scale, you should look into [TileDB-VC…
Answer: Dealing with missing (NA) values in my 450K methylation array dataset
by
Basti
★ 1.3k
You could omit the NA values : `pca <- prcomp(na.omit(t(exprs(GSE65820))))`
Comment: Virtual box
by
Ram
37k
This post does not fit the theme of this forum.
Comment: Filter InterProScan output for a specific function
by
jv
▴ 780
I imagine you can filter on things like E.C. numbers and domain names using `bash`, `awk`, `R`, or some other code.
Comment: How to find the most frequent alternative-splicing event from DEXSEQ data?
by
STARDUST
• 0
I will try both rMATS and SUPPA for categorising changes. For the specific exons, i'm expecting the last exons should be affected. That is …
Answer: snp Caenorhabditis elegans
by
GenoMax
125k
See: https://www.elegansvariation.org/data/release/20220216
Answer: want the codes for cuffdiff , NIOSeq , bayseq to perform DEGs.
by
jv
▴ 780
- NOISeq <https://www.bioconductor.org/packages/release/bioc/vignettes/NOISeq/inst/doc/NOISeq.pdf> - Cuffdiff <http://cole-trapnell-lab.gi…
Comment: fastqc: Per base sequence content
by
jv
▴ 780
I think this is to be expected based a report I was able to find online <https://uu.diva-portal.org/smash/get/diva2:1608120/FULLTEXT01.pd…
Comment: fastqc: Per base sequence content
by
GenoMax
125k
Unless the kit directions tell you to remove remove the initial 10-15 bp you may as well leave them alone. Data should align would be my in…
Comment: RNA Editing data from RNA-seq
by
Genetics
• 0
Thank you so much for your kind reply and for helping a bioinformatics beginner like me. Can I use **bowtie2** tools for allignment and th…
Comment: fastqc: Per base sequence content
by
khoojj
• 0
Yes, I have proceed with analysis but I wonder if it is necessary to remove the first 10 or so bp from the reads. I have checked that NEBN…
Comment: Novogene somatic results with GATK mutect2
by
GenoMax
125k
Did you look in the header of the provided VCF to see if any information has been encoded there (e.g. command line/options used).
Comment: RNASeq differential expression masked by pathways disregulation
by
Gama313
▴ 110
That's exactly what I've done. However the dispersion is really high (primary samples) and the total number of samples seems really low to…
Comment: fastqc: Per base sequence content
by
GenoMax
125k
If the library was made using tagmentation then you will see that pattern. Flag warnings on FastQC do not immediately indicate that the da…
Answer: What type of database does gnomAD use?
by
Matthias Zepper
2.9k
I suppose there are multiple? Queries via Hail are very likely run against a [Matrix Table][1], but the web application likely uses a diffe…
Traffic: 3174 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