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1,000 results • Page
1 of 20
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
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
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
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
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
2
replies
199
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
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
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
1
reply
114
views
Freyja plot error
Freyja
updated 15 hours ago by
Ram
43k • written 20 hours ago by
Adyasha
• 0
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
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
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
0
votes
0
replies
111
views
what exactly is a k-mer table (remora)?
remora
basecall
1 day ago by
anne
• 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
113
views
GWAS Phenotypes
GWAS
1 day ago by
solomoncharles77
▴ 90
0
votes
1
reply
171
views
GSEA analysis in R
GSEA
R
Arabidopsis
updated 1 day ago by
sansan_96
▴ 80 • written 1 day ago by
Sudip
• 0
0
votes
0
replies
98
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
1 day ago by
QX
• 0
2
votes
5
replies
317
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
23 hours ago by
Bikram Kumar
• 0
0
votes
2
replies
215
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 1 day ago by
Ram
43k • written 2 days ago by
David
• 0
1
vote
2
replies
223
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
1 day ago by
bioinfo
▴ 150
0
votes
1
reply
164
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 2 days ago by
bk11
★ 2.3k • written 2 days ago by
sinhas
• 0
0
votes
1
reply
180
views
merging Seurat objects after SCT
Seurat
SCT
updated 2 days ago by
Ram
43k • written 2 days ago by
michelle.swarovski
• 0
0
votes
1
reply
155
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 2 days ago by
GenoMax
141k • written 2 days ago by
haiying.kong
▴ 360
0
votes
2
replies
229
views
RNAseq 1 control 2 different treatment
RNA-seq
1 day ago by
matteo.levorato
• 0
1
vote
0
replies
120
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 2 days ago by
Ram
43k • written 2 days ago by
Oscar
▴ 10
0
votes
0
replies
124
views
How should I make kallisto indexes?
kallisto
updated 2 days ago by
GenoMax
141k • written 2 days ago by
bioinfo
▴ 150
2
votes
0
replies
176
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
2 days ago by
Alexander
▴ 220
1
vote
1
reply
149
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 2 days ago by
GenoMax
141k • written 2 days ago by
eesiribloom
▴ 80
0
votes
0
replies
111
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
2 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
115
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
2 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
125
views
FreeBayes detection capacity
reads
freebayes
long
2 days ago by
quentinperriere
• 0
0
votes
2
replies
198
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
18 hours ago by
DKA
▴ 40
0
votes
2
replies
224
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
2 days ago by
rj.rezwan
• 0
0
votes
0
replies
145
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
3 days ago by
Hien
• 0
0
votes
2
replies
253
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
1 day ago by
Koketso
• 0
0
votes
0
replies
173
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 3 days ago by
Ram
43k • written 3 days ago by
menyawino
• 0
1
vote
3
replies
300
views
Ensembl gene id conversion
biomart
ensembl
updated 1 day ago by
ATpoint
81k • written 3 days ago by
naveedhasan2000
• 0
1
vote
2
replies
286
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 2 days ago by
Istvan Albert
100k • written 4 days ago by
Jiang
• 0
0
votes
0
replies
171
views
Core SNP tree VS. concatenated core genome tree
phylogenetic
tree
SNP
4 days ago by
YiweiZhu
▴ 30
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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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