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 : all time
all time
today
this week
this month
this year
116,475 results • Page
2 of 2330
Sort: Rank
Rank
Views
Votes
Replies
2
votes
2
replies
344
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
17 hours ago by
nhaus
▴ 300
0
votes
0
replies
263
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
1 day ago by
Ronin
• 0
4
votes
2
replies
1.7k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 1 day ago by
Dr.Animo
▴ 130 • written 11 months ago by
BioinfoBee
• 0
2
votes
7
replies
682
views
Removing duplicates
duplicates
ONT
minimap2
updated 10 hours ago by
joe
▴ 500 • written 1 day ago by
quentinperriere
• 0
0
votes
1
reply
164
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 1 day ago by
DKA
▴ 40 • written 1 day ago by
james.melhorn
• 0
3
votes
4
replies
347
views
biomaRt error for different R version
biomaRt
R
updated 21 hours ago by
GenoMax
141k • written 1 day ago by
manaswwm
▴ 490
0
votes
1
reply
153
views
Freyja plot error
Freyja
updated 1 day ago by
Ram
43k • written 2 days ago by
Adyasha
• 0
1
vote
2
replies
160
views
Interpretation of combined P values - RNA microarray meta analysis
metaanalysis
R
microarray
DExMA
combinedP
2 days ago by
hagl
▴ 10
0
votes
0
replies
121
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
2 days ago by
chemokine-1
▴ 10
0
votes
4
replies
419
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
1 day ago by
feather-W
• 0
0
votes
0
replies
184
views
Job:
Consultant to update a Snakemake workflow with the new Kubernetes executor plugin for Snakemake 8
Kubernetes
DevOps
executor
AWS
Snakemake
updated 2 days ago by
Michael
54k • written 2 days ago by
jonrkarr
▴ 100
0
votes
2
replies
183
views
Bedmethyl file format
bedmethyl
methylation
updated 1 day ago by
GenoMax
141k • written 2 days ago by
njornet
▴ 20
0
votes
0
replies
137
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
2 days ago by
Ali
• 0
2
votes
4
replies
269
views
SnpEff annotates coding duplication as intronic?
snpeff
2 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
209
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
1 day ago by
mropri
▴ 150
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq
breast cancer
subtyping
updated 2 days ago by
hamarillo
▴ 70 • written 5.6 years ago by
silviajserrano
▴ 50
3
votes
10
replies
574
views
Piping samtools to R
R
NGS
bash
samtools
2 days ago by
joe
▴ 500
2
votes
2
replies
207
views
How to filter columns in a raw sparse matrix in R
matrix
R
updated 2 days ago by
bk11
★ 2.3k • written 2 days ago by
bgbs
• 0
3
votes
7
replies
377
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq
tmt
nomenclature
proteomics
2 days ago by
ntsopoul
▴ 60
0
votes
0
replies
124
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
2 days ago by
shasabhi1
• 0
0
votes
0
replies
120
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
2 days ago by
Nishat
• 0
3
votes
3
replies
377
views
trouble using sequenceTubeMap in chromium installed on WSL
vg
2 days ago by
ayushm64
• 0
0
votes
0
replies
132
views
what exactly is a k-mer table (remora)?
remora
basecall
2 days ago by
anne
• 0
3
votes
6
replies
10k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 2 days ago by
Bioinfotec
▴ 10 • written 7.5 years ago by
nut_B
▴ 10
1
vote
6
replies
338
views
Rename multiple fastq.gz files
fastq
next-gen
updated 2 days ago by
shenwei356
8.4k • written 2 days ago by
Jérémie
• 0
1
vote
1
reply
154
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 2 days ago by
dsull
★ 5.8k • written 2 days ago by
niruf
• 0
0
votes
0
replies
155
views
Job:
Ensembl Outreach Project Leader
ebi
embl
genomics
ensembl
2 days ago by
Ben_Ensembl
★ 2.4k
2
votes
3
replies
240
views
Bwa sampe - BGI
Bwa-sampe
BGI
updated 2 days ago by
GenoMax
141k • written 2 days ago by
lorena9132
• 0
0
votes
0
replies
154
views
News:
Final Call - Bioinformatics Pipeline Development with Nextflow (May 27-29, 2024)
workshop
RNA-seq
nextflow
DNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
David Langenberger
11k
0
votes
0
replies
126
views
GWAS Phenotypes
GWAS
2 days ago by
solomoncharles77
▴ 90
4
votes
2
replies
232
views
Forum:
Bioinformatics: Where do I start
Sequencing
updated 2 days ago by
Ram
43k • written 2 days ago by
Adi
▴ 10
0
votes
2
replies
281
views
GSEA analysis in R
GSEA
R
Arabidopsis
1 day ago by
Sudip
• 0
1
vote
2
replies
232
views
Visualization of PROKKA Annotation Result?
PROKKA
Annotation
updated 2 days ago by
Joe
21k • written 3 days ago by
ferdinand
▴ 10
0
votes
2
replies
342
views
Which experiments generate Position Frequency Matrix?
Position-Frequency-Matrix
1 day ago by
arriyaz.nstu
▴ 30
2
votes
2
replies
353
views
I am new to single cell analysis. Can RNA velocity (spliced/unspliced) be calculated solely from the raw file (count matrix) provided in the Suppleme…
GEO
velocity
count-matrix
updated 2 days ago by
Ram
43k • written 3 days ago by
Spring
• 0
0
votes
0
replies
106
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
3 days ago by
QX
• 0
5
votes
4
replies
249
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger
scRNA-seq
10x
3 days ago by
Spring
• 0
2
votes
5
replies
344
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
2 days ago by
Bikram Kumar
• 0
1
vote
1
reply
273
views
WGCNA network from Adjacency or TOM matrix
WGCNA
network
updated 3 days ago by
andres.firrincieli
3.6k • written 6 days ago by
Milly
• 0
0
votes
1
reply
197
views
Error in edgeR/Deseq2 Analysis
r
edger
updated 3 days ago by
ATpoint
81k • written 3 days ago by
Ravita
• 0
0
votes
2
replies
202
views
Getting marker genes for cell types
clustering
marker-genes
umap
3 days ago by
orzrzlyo
▴ 20
0
votes
1
reply
196
views
gene body coverage with RSeqQC
rna-seq
qc
updated 2 days ago by
BioinfGuru
★ 1.7k • written 3 days ago by
wiscoyogi
▴ 40
0
votes
2
replies
226
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 2 days ago by
Ram
43k • written 3 days ago by
David
• 0
0
votes
1
reply
174
views
Using adonis to include a random effect
mixed-model
adonis
updated 3 days ago by
LChart
3.9k • written 3 days ago by
leranwangcs
▴ 120
1
vote
3
replies
397
views
how to get the variance explained by the independent variable from multivariate distance matrix regression model with random effect?
multivariate-distance-matrix
regression
updated 3 days ago by
LChart
3.9k • written 4 days ago by
leranwangcs
▴ 120
1
vote
2
replies
232
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
2 days ago by
bioinfo
▴ 150
0
votes
1
reply
170
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 3 days ago by
bk11
★ 2.3k • written 3 days ago by
sinhas
• 0
1
vote
5
replies
323
views
Best way to deal with overlapping read names in merged BAM files
picard
MarkDuplicates
3 days ago by
shpak.max
▴ 50
0
votes
1
reply
188
views
merging Seurat objects after SCT
Seurat
SCT
updated 3 days ago by
Ram
43k • written 3 days ago by
michelle.swarovski
• 0
0
votes
1
reply
167
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 3 days ago by
GenoMax
141k • written 3 days ago by
haiying.kong
▴ 360
116,475 results • Page
2 of 2330
Recent Votes
DNA Methylation: Sequencing Techniques
Comment: How to install Guppy from Nanopore Technologies?
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR
Answer: Indexing the Reference Genome is not done in STAR
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
How to compare the quality of assemblies
Recent Locations •
All
United States,
just now
France,
just now
Spain,
just now
United Kingdom,
1 minute ago
India,
2 minutes ago
Germany,
2 minutes ago
France,
2 minutes ago
Recent Awards •
All
Popular Question
to
biwdpang
• 0
Popular Question
to
Michael
54k
Scholar
to
Gordon Smyth
★ 7.0k
Popular Question
to
yueli7
▴ 250
Popular Question
to
Chirag Parsania
★ 2.0k
Scholar
to
LChart
3.9k
Scholar
to
swbarnes2
14k
Recent Replies
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file
by
Maria
• 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis
by
Michael
54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
Pierre Lindenbaum
161k
> server so I cannot use Blat for this purpose. blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
b.contreras.moreira
▴ 160
My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`. It is…
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software
by
colindaven
6.3k
Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
Hagen
▴ 10
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
Comment: Per base sequence content failed miserably
by
Kai Xin
• 0
will look into that. Thank you very much
Comment: Korean human genome reference file
by
SeoGyun
• 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool
by
Ashok
• 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
by
cmdcolin
★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB
by
航太郎
• 0
Thanks for your guide!
Comment: Removing duplicates
by
joe
▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis
by
swbarnes2
14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file
by
swbarnes2
14k
Shouldn't you use PicardTools for this?
Traffic: 2706 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