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101 results • Page
1 of 3
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0
votes
0
replies
1
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Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
just now by
ekirsch
• 0
0
votes
0
replies
50
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
4 hours ago by
renan.igor
• 0
0
votes
1
reply
113
views
Pediococcus acidilactici sequence analysis
BLAST
Gene-Ontology
updated 28 minutes ago by
Ram
43k • written 6 hours ago by
anasjamshed
▴ 120
2
votes
1
reply
502
views
What is the normalization status of metabric data?
metabric
normalization
microarray
cbioportal
updated 5 hours ago by
etiennedanis
▴ 10 • written 19 months ago by
DareDevil
★ 4.3k
0
votes
0
replies
51
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
6 hours ago by
synat.keam
▴ 100
0
votes
1
reply
127
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 8 hours ago by
GenoMax
141k • written 8 hours ago by
ycts
• 0
1
vote
3
replies
303
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
updated 9 hours ago by
swbarnes2
14k • written 11 hours ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
168
views
Inconsistency in SNP detection pipelines for multi-sample analysis
vcf
bam
bcf
snps
updated 10 hours ago by
LChart
3.9k • written 12 hours ago by
George
▴ 10
0
votes
0
replies
74
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
updated 10 hours ago by
Ram
43k • written 10 hours ago by
otieno43
▴ 20
0
votes
1
reply
147
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
updated 11 hours ago by
GenoMax
141k • written 11 hours ago by
Kai Xin
• 0
1
vote
1
reply
134
views
Retrieve a % coverage for each transcript
RNA-seq
updated 12 hours ago by
Ram
43k • written 12 hours ago by
jammydodger123456
▴ 40
0
votes
1
reply
260
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 12 hours ago by
Klaus S
▴ 150 • written 5 days ago by
Zeng Hao
▴ 40
0
votes
2
replies
178
views
How can I solve this error?
metal
2 hours ago by
22211020193
• 0
0
votes
0
replies
78
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 12 hours ago by
GenoMax
141k • written 13 hours ago by
srimmer
• 0
1
vote
2
replies
169
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 11 hours ago by
Ram
43k • written 13 hours ago by
aniigodwinn
• 0
0
votes
2
replies
173
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
updated 13 hours ago by
colindaven
6.3k • written 18 hours ago by
valentinatsar
• 0
1
vote
3
replies
177
views
Editing Human Reference Genome by adding a CDS
gff
agat
transcriptome
updated 13 hours ago by
Michael
54k • written 14 hours ago by
LDT
▴ 330
0
votes
8
replies
338
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 12 hours ago by
Pierre Lindenbaum
161k • written 15 hours ago by
me
• 0
0
votes
1
reply
196
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
updated 16 hours ago by
Gordon Smyth
★ 7.0k • written 8 days ago by
nhaus
▴ 300
0
votes
0
replies
113
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
16 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 17 hours ago by
Dr.Animo
▴ 130 • written 11 months ago by
BioinfoBee
• 0
0
votes
5
replies
388
views
Removing duplicates
duplicates
ONT
minimap2
updated 3 hours ago by
joe
▴ 490 • written 18 hours ago by
quentinperriere
• 0
0
votes
1
reply
122
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 17 hours ago by
DKA
▴ 40 • written 18 hours ago by
james.melhorn
• 0
0
votes
3
replies
184
views
biomaRt error for different R version
biomaRt
R
updated 15 hours ago by
Mike Smith
★ 2.0k • written 19 hours ago by
manaswwm
▴ 490
0
votes
1
reply
110
views
Freyja plot error
Freyja
updated 14 hours ago by
Ram
43k • written 19 hours ago by
Adyasha
• 0
1
vote
2
replies
126
views
Interpretation of combined P values - RNA microarray meta analysis
metaanalysis
R
microarray
DExMA
combinedP
20 hours ago by
hagl
▴ 10
0
votes
0
replies
75
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
21 hours ago by
chemokine-1
▴ 10
0
votes
2
replies
185
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
2 hours ago by
feather-W
• 0
0
votes
1
reply
140
views
Job:
Consultant to update a Snakemake workflow with the new Kubernetes executor plugin for Snakemake 8
Kubernetes
DevOps
executor
AWS
Snakemake
updated 19 hours ago by
Michael
54k • written 21 hours ago by
jonrkarr
▴ 100
0
votes
2
replies
144
views
Bedmethyl file format
bedmethyl
methylation
updated 17 hours ago by
GenoMax
141k • written 21 hours ago by
njornet
▴ 20
0
votes
0
replies
96
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
21 hours ago by
Ali
• 0
2
votes
4
replies
237
views
SnpEff annotates coding duplication as intronic?
snpeff
23 hours ago by
kirill.zaslavsky
• 0
0
votes
2
replies
170
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
18 hours ago by
mropri
▴ 150
0
votes
1
reply
184
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
updated 12 hours ago by
bk11
★ 2.3k • written 1 day ago by
航太郎
• 0
0
votes
2
replies
327
views
Which experiments generate Position Frequency Matrix?
Position-Frequency-Matrix
13 hours ago by
arriyaz.nstu
▴ 30
2
votes
5
replies
316
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
22 hours ago by
Bikram Kumar
• 0
6
votes
8
replies
438
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 19 hours ago by
dariober
14k • written 2 days ago by
manaswiniparija3
▴ 40
0
votes
2
replies
198
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
17 hours ago by
DKA
▴ 40
85
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 3 hours ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
1
vote
2
replies
317
views
Forum:
VCF bulk handling
bcftools
SnpEff
WGS
VEP
VCF
17 hours ago by
Javier
• 0
1
vote
3
replies
253
views
Merging vcf files with bcftools ([E::get_intv] Failed to parse TBX_VCF, was wrong -p [type] used?)
vcf
tabix
bcftools
updated 19 hours ago by
Pierre Lindenbaum
161k • written 6 days ago by
giulia.cosenza
• 0
7
votes
5
replies
3.4k
views
ISCN annotation for SV/CN VCF files
SV
updated 1 hour ago by
adedare
• 0 • written 7 months ago by
a.beggs
▴ 50
2
votes
2
replies
870
views
Method to detect genome doubling
CNV
genome doubling
updated 12 hours ago by
Zhenyu Zhang
★ 1.2k • written 4.4 years ago by
CY
▴ 750
1
vote
8
replies
1.0k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 11 hours ago by
GenoMax
141k • written 19 months ago by
Gerard
▴ 10
8
votes
6
replies
2.5k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 7 hours ago by
John Marshall
3.0k • written 23 months ago by
bioguy24
▴ 230
1
vote
2
replies
1.4k
views
How to download a list pdb codes contained in a csv file using
Biopython
updated 23 hours ago by
Ram
43k • written 3.1 years ago by
jmungar2
▴ 10
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov
scatter-plot
anova
updated 23 hours ago by
Ram
43k • written 3.1 years ago by
Rob
▴ 170
3
votes
2
replies
798
views
Retrieve initial query in getBM()
getBM
biomaRt
R
gene
updated 23 hours ago by
Ram
43k • written 3.1 years ago by
helia.ziaei
• 0
2
votes
2
replies
1.6k
views
How to add a title to a cnetplot?
r
cnetplot
updated 23 hours ago by
Ram
43k • written 3.4 years ago by
appropiate
▴ 80
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt
R
updated 23 hours ago by
Ram
43k • written 3.8 years ago by
mbk0asis
▴ 680
101 results • Page
1 of 3
Recent Votes
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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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…
Comment: Supergnova stuck in tutorial
by
GenoMax
141k
Your best option may be to email the author (and/or the senior author from the paper). Let them know that the FTP links mentioned on GitHub…
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