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195 results • Page
4 of 4
Sort: Votes
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Views
Votes
Replies
0
votes
1
reply
145
views
RNA-seq bacteria contamination
RNA-seq
updated 3 days ago by
GenoMax
141k • written 3 days ago by
sh
• 0
0
votes
0
replies
82
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
3 days ago by
manaswwm
▴ 490
0
votes
1
reply
119
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 3 days ago by
ATpoint
82k • written 3 days ago by
enanoide
• 0
0
votes
0
replies
202
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
3 days ago by
Javier
• 0
0
votes
1
reply
124
views
tbtool
tbtool
updated 3 days ago by
Ram
43k • written 3 days ago by
Raman
• 0
0
votes
2
replies
187
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 3 days ago by
i.sudbery
19k • written 3 days ago by
Patadu94
• 0
0
votes
0
replies
89
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 3 days ago by
Ram
43k • written 3 days ago by
sansan_96
▴ 80
0
votes
0
replies
175
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 3 days ago by
Ram
43k • written 3 days ago by
Oak
▴ 10
0
votes
0
replies
273
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 3 days ago by
Ram
43k • written 14 months ago by
Oak
▴ 10
0
votes
0
replies
105
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 3 days ago by
Ram
43k • written 3 days ago by
maxime.policarpo
▴ 200
0
votes
1
reply
140
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 2 days ago by
Ram
43k • written 3 days ago by
Cameron.walker9900
• 0
0
votes
2
replies
170
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
2 days ago by
sainavyav22
• 0
0
votes
8
replies
293
views
Error in cnetplot enrichplot package
R
updated 2 days ago by
Ram
43k • written 3 days ago by
Farhad
• 0
0
votes
0
replies
157
views
Forum:
Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation
scRNA
llm
2 days ago by
yxwucq
• 0
0
votes
3
replies
478
views
python file for coding potential calculator
cpc2.py
updated 2 days ago by
atharvakarkare14
▴ 10 • written 7 days ago by
Ashok
• 0
0
votes
0
replies
73
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
2 days ago by
alifafiq1
• 0
0
votes
0
replies
93
views
Merging replicates from Encode project
CHIP-seq
encode
2 days ago by
Nurken
• 0
0
votes
1
reply
125
views
Plots for DNA methylation data
plots
DNA
methylation
updated 2 days ago by
GenoMax
141k • written 2 days ago by
sarahawan92
▴ 10
0
votes
3
replies
363
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 2 days ago by
colindaven
6.4k • written 10 days ago by
rj.rezwan
• 0
0
votes
3
replies
196
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 2 days ago by
mchour
• 0 • written 2 days ago by
rhossen
• 0
0
votes
1
reply
148
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Srinka
▴ 20
0
votes
0
replies
84
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 2 days ago by
Ram
43k • written 2 days ago by
SHREYA
• 0
0
votes
0
replies
92
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 2 days ago by
Ram
43k • written 3 days ago by
Amélie
• 0
0
votes
1
reply
125
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 2 days ago by
bk11
★ 2.3k • written 2 days ago by
Susmita Mandal
▴ 110
0
votes
0
replies
91
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
2 days ago by
ohtang7
▴ 40
0
votes
0
replies
81
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 2 days ago by
Ram
43k • written 2 days ago by
SSSJec
• 0
0
votes
1
reply
145
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 2 days ago by
bk11
★ 2.3k • written 2 days ago by
alphaflylizard
• 0
0
votes
6
replies
292
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
1 day ago by
Sd
• 0
0
votes
3
replies
226
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
updated 1 day ago by
Istvan Albert
100k • written 2 days ago by
Dylan
• 0
0
votes
1
reply
194
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 1 day ago by
Istvan Albert
100k • written 3 days ago by
Abeer
• 0
0
votes
4
replies
275
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 1 day ago by
swbarnes2
14k • written 3 days ago by
dxj294
• 0
0
votes
0
replies
101
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
1 day ago by
Kash
▴ 110
0
votes
10
replies
395
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
1 day ago by
atowns21
• 0
0
votes
1
reply
137
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
benguyarenbeyaz98
• 0
0
votes
6
replies
424
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 1 day ago by
gv
• 0 • written 24 days ago by
Srinka
▴ 20
0
votes
0
replies
108
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
1 day ago by
salias
• 0
0
votes
5
replies
280
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
1 day ago by
njornet
▴ 20
0
votes
14
replies
3.5k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 1 day ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
0
votes
2
replies
203
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
1 day ago by
mropri
▴ 150
0
votes
0
replies
198
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
1 day ago by
pramach1
▴ 40
0
votes
0
replies
88
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
variantcalling
DNAseq
illumina
RNAseq
transcriptomics
1 day ago by
David Langenberger
11k
0
votes
1
reply
124
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 1 day ago by
Sofia
• 0 • written 1 day ago by
mawigoj318
• 0
0
votes
2
replies
768
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 1 day ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
0
replies
106
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 1 day ago by
Ram
43k • written 1 day ago by
glaciya2018
• 0
0
votes
0
replies
98
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 1 day ago by
Ram
43k • written 1 day ago by
newuser2024
• 0
195 results • Page
4 of 4
Recent Votes
Answer: Sequence read length shorter than flow cell specification
Answer: Sequence read length shorter than flow cell specification
Comment: Why gatk VariantAnnotator required bam and coverage files
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Answer: How do I get the 3bp sequence on either side of a co-ordinate
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Recent Replies
Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
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▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases
by
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141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases
by
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11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
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by
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I think when you give indent to seuObj : Idents(seuObj) <- 'RNA_snn_res.0.1' You may wrongly assign other value to it such as …
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by
Bioinfotec
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In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
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by
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▴ 10
In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
Comment: Sequence read length shorter than flow cell specification
by
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141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
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▴ 840
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification
by
ATpoint
82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator : VariantAnnotator …
Comment: GAPIT p-value significance threshold
by
ginellegrenier
• 0
Hi, I was wondering if you have found a solution to this? Thanks!
Comment: PCA plot
by
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▴ 170
cross posted in bioconductor. [https://support.bioconductor.org/p/9157968/][1] [1]: https://support.bioconductor.org/p/9157968/
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by
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★ 2.3k
Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
Comment: How to make a TSS enrichment plot in ATAC-seq analysis?
by
sp
• 0
Hi Dan, I was wondering if you found out how to make the same graph with NFR and NBR regions with different curves. I was able to recreate…
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