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116,448 results • Page
1 of 2329
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0
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16
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
1 hour ago by
ekirsch
• 0
0
votes
0
replies
58
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
5 hours ago by
renan.igor
• 0
0
votes
1
reply
122
views
Pediococcus acidilactici sequence analysis
BLAST
Gene-Ontology
updated 1 hour ago by
Ram
43k • written 7 hours ago by
anasjamshed
▴ 120
2
votes
1
reply
510
views
What is the normalization status of metabric data?
metabric
normalization
microarray
cbioportal
updated 6 hours ago by
etiennedanis
▴ 10 • written 19 months ago by
DareDevil
★ 4.3k
0
votes
0
replies
57
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
7 hours ago by
synat.keam
▴ 100
795
votes
167
replies
141k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 12 weeks ago by
Biostar
2.6k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
136
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 9 hours ago by
GenoMax
141k • written 9 hours ago by
ycts
• 0
1
vote
3
replies
319
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
updated 10 hours ago by
swbarnes2
14k • written 13 hours ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
174
views
Inconsistency in SNP detection pipelines for multi-sample analysis
vcf
bam
bcf
snps
updated 11 hours ago by
LChart
3.9k • written 13 hours ago by
George
▴ 10
0
votes
0
replies
79
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
updated 11 hours ago by
Ram
43k • written 11 hours ago by
otieno43
▴ 20
0
votes
1
reply
153
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
updated 12 hours ago by
GenoMax
141k • written 12 hours ago by
Kai Xin
• 0
1
vote
1
reply
140
views
Retrieve a % coverage for each transcript
RNA-seq
updated 13 hours ago by
Ram
43k • written 13 hours ago by
jammydodger123456
▴ 40
0
votes
1
reply
263
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 13 hours ago by
Klaus S
▴ 150 • written 5 days ago by
Zeng Hao
▴ 40
0
votes
2
replies
204
views
How can I solve this error?
metal
3 hours ago by
22211020193
• 0
0
votes
0
replies
81
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 13 hours ago by
GenoMax
141k • written 14 hours ago by
srimmer
• 0
1
vote
2
replies
173
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 12 hours ago by
Ram
43k • written 14 hours ago by
aniigodwinn
• 0
0
votes
2
replies
179
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
updated 14 hours ago by
colindaven
6.3k • written 19 hours ago by
valentinatsar
• 0
1
vote
3
replies
183
views
Editing Human Reference Genome by adding a CDS
gff
agat
transcriptome
updated 14 hours ago by
Michael
54k • written 15 hours ago by
LDT
▴ 330
0
votes
8
replies
345
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 13 hours ago by
Pierre Lindenbaum
161k • written 16 hours ago by
me
• 0
0
votes
1
reply
197
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
updated 17 hours ago by
Gordon Smyth
★ 7.0k • written 8 days ago by
nhaus
▴ 300
0
votes
0
replies
121
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
17 hours ago by
Ronin
• 0
4
votes
2
replies
1.6k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 19 hours ago by
Dr.Animo
▴ 130 • written 11 months ago by
BioinfoBee
• 0
0
votes
5
replies
402
views
Removing duplicates
duplicates
ONT
minimap2
updated 4 hours ago by
joe
▴ 490 • written 19 hours ago by
quentinperriere
• 0
0
votes
1
reply
127
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 18 hours ago by
DKA
▴ 40 • written 20 hours ago by
james.melhorn
• 0
0
votes
3
replies
190
views
biomaRt error for different R version
biomaRt
R
updated 16 hours ago by
Mike Smith
★ 2.0k • written 20 hours ago by
manaswwm
▴ 490
0
votes
1
reply
114
views
Freyja plot error
Freyja
updated 15 hours ago by
Ram
43k • written 20 hours ago by
Adyasha
• 0
1
vote
2
replies
130
views
Interpretation of combined P values - RNA microarray meta analysis
metaanalysis
R
microarray
DExMA
combinedP
21 hours ago by
hagl
▴ 10
0
votes
0
replies
81
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
22 hours ago by
chemokine-1
▴ 10
0
votes
3
replies
217
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
updated 28 minutes ago by
LChart
3.9k • written 22 hours ago by
feather-W
• 0
0
votes
1
reply
145
views
Job:
Consultant to update a Snakemake workflow with the new Kubernetes executor plugin for Snakemake 8
Kubernetes
DevOps
executor
AWS
Snakemake
updated 21 hours ago by
Michael
54k • written 22 hours ago by
jonrkarr
▴ 100
0
votes
2
replies
150
views
Bedmethyl file format
bedmethyl
methylation
updated 18 hours ago by
GenoMax
141k • written 22 hours ago by
njornet
▴ 20
0
votes
0
replies
101
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
23 hours ago by
Ali
• 0
2
votes
4
replies
240
views
SnpEff annotates coding duplication as intronic?
snpeff
1 day ago by
kirill.zaslavsky
• 0
0
votes
2
replies
174
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
19 hours ago by
mropri
▴ 150
0
votes
1
reply
189
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
updated 13 hours ago by
bk11
★ 2.3k • written 1 day ago by
航太郎
• 0
5
votes
4
replies
2.7k
views
genefu for PAM50 prediction
RNA-Seq
breast cancer
subtyping
updated 1 day ago by
hamarillo
▴ 70 • written 5.6 years ago by
silviajserrano
▴ 50
3
votes
10
replies
549
views
Piping samtools to R
R
NGS
bash
samtools
1 day ago by
joe
▴ 490
2
votes
2
replies
187
views
How to filter columns in a raw sparse matrix in R
matrix
R
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
bgbs
• 0
3
votes
7
replies
348
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq
tmt
nomenclature
proteomics
1 day ago by
ntsopoul
▴ 60
0
votes
0
replies
104
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
1 day ago by
shasabhi1
• 0
0
votes
0
replies
98
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
1 day ago by
Nishat
• 0
3
votes
3
replies
358
views
trouble using sequenceTubeMap in chromium installed on WSL
vg
1 day ago by
ayushm64
• 0
0
votes
0
replies
111
views
what exactly is a k-mer table (remora)?
remora
basecall
1 day ago by
anne
• 0
3
votes
6
replies
10k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 1 day ago by
Bioinfotec
▴ 10 • written 7.5 years ago by
nut_B
▴ 10
1
vote
6
replies
318
views
Rename multiple fastq.gz files
fastq
next-gen
updated 1 day ago by
shenwei356
8.4k • written 1 day ago by
Jérémie
• 0
1
vote
1
reply
144
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 1 day ago by
dsull
★ 5.8k • written 1 day ago by
niruf
• 0
0
votes
0
replies
134
views
Job:
Ensembl Outreach Project Leader
ebi
embl
genomics
ensembl
1 day ago by
Ben_Ensembl
★ 2.4k
2
votes
3
replies
219
views
Bwa sampe - BGI
Bwa-sampe
BGI
updated 1 day ago by
GenoMax
141k • written 1 day ago by
lorena9132
• 0
0
votes
0
replies
130
views
News:
Final Call - Bioinformatics Pipeline Development with Nextflow (May 27-29, 2024)
workshop
RNA-seq
nextflow
DNA-seq
updated 1 day ago by
Ram
43k • written 1 day ago by
David Langenberger
11k
0
votes
0
replies
114
views
GWAS Phenotypes
GWAS
1 day ago by
solomoncharles77
▴ 90
116,448 results • Page
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High fold change values
C: Bcftools Mpileup Removes Marked Duplicates?
Prediction tools summary - zero values
A: Error with Formatdb of legacy blast?
Error with Formatdb of legacy blast?
Answer: How to convert SAM/BAM file to GTF/GFF file?
A: Ribo-seq vs RNA-seq read count
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Recent Replies
Comment: How to reduce the variation of CIBERSORTx results?
by
LChart
3.9k
First time I've heard of S-mode. I imagine you've seen this benchmark where it doesn't come out too well: https://academic.oup.com/bib/arti…
Comment: ISCN annotation for SV/CN VCF files
by
adedare
• 0
https://res.saletool.cn/vcf/18084521725806
Comment: ISCN annotation for SV/CN VCF files
by
adedare
• 0
https://res.saletool.cn/vcf/18084435127462
Comment: How can I solve this error?
by
22211020193
• 0
I want to conduct GWAS meta-analysis using metal software.
Comment: How to reduce the variation of CIBERSORTx results?
by
feather-W
• 0
Hi LChart, Thanks for your reply. Yes, the identical command lines produce different results in CIBERSORTx S-mode. Although I input the da…
Comment: Removing duplicates
by
joe
▴ 490
I *could* imagine an ONT scenario where you'd want to remove duplicates (amplicon-seq, etc) but likely for variant calling there is no need…
Comment: Removing duplicates
by
samuel.a.odonnell
▴ 510
As above, you do not need to worry about duplicates for ONT data Also have you looked at using other tools for variant calling more suited…
Answer: Pediococcus acidilactici sequence analysis
by
geneontologyhelp
▴ 340
If you're looking for the GO annotations for *Pediococcus acidilactici*, these are available. Using the instructions under [*2. All other…
Answer: What is the normalization status of metabric data?
by
etiennedanis
▴ 10
I just found an answer to this question here: [https://groups.google.com/g/cbioportal/c/hm_i4jbG1uc/m/h9rNYOvpAAAJ][1] [1]: https://gro…
Comment: Removing duplicates
by
joe
▴ 490
With ONT you will only have PCR duplicates. 'Read' (you mean optical?) duplicates are an artifact of cluster-based sequencing (ie Illumina)…
Comment: assembly using CCS, CLR, CCS_CLR sequences together?
by
GenoMax
141k
PacBio has some recommendations on software for genome assemblies on this page (which you may have seen but just in case): https://www.pacb…
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
swbarnes2
14k
I would not put totally different tissues in the same DESeq object. I don't think that's going to do good things for normalization or disp…
Comment: Removing duplicates
by
quentinperriere
• 0
pcr duplicates or/and read duplicates should I use this command to remove them ? or we don't talk about duplicates when dealing with ONT ??…
Comment: How to reduce the variation of CIBERSORTx results?
by
LChart
3.9k
If you didn't change the input signature matrix, the input RNA matrix, or the input parameters - what did you change? Is the statement that…
Answer: Inconsistency in SNP detection pipelines for multi-sample analysis
by
LChart
3.9k
> To replicate GVCF behavior and avoid issues with 0/0 genotypes appearing as missing, I don't use the -v option I'm not sure what you m…
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