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184 results • Page 3 of 4
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0
votes
2
replies
214
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 1 day ago by 43k • written 2 days ago by ▴ 10
2
votes
1
reply
213
views
Finding orthologs between genome error
OMA OMAbrowser
updated 2 days ago by ★ 1.1k • written 3 days ago by • 0
0
votes
1
reply
211
views
Network Alignment
plugin Cytoscape CytoMCS
updated 3 days ago by ▴ 280 • written 4 days ago by ▴ 40
1
vote
1
reply
210
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting blast
updated 4 days ago by 100k • written 5 days ago by • 0
2
votes
3
replies
207
views
from row count to tpm
tpm row-count normalization
5 days ago by michelafrancesconi9 ▴ 20
0
votes
0
replies
205
views
traying to make a maf from an already annotated vcf
vcf vcf2maf maf maftools VEP
5 days ago by Javier • 0
3
votes
3
replies
203
views
Genbank vs SRA
ncbi genbank genomics sra
updated 5 days ago by ★ 27k • written 5 days ago by ▴ 520
0
votes
0
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199
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS Meta-analysis
updated 5 days ago by 43k • written 5 days ago by ▴ 10
0
votes
2
replies
195
views
Result of running of p3_in.pl
primer3
updated 5 days ago by 141k • written 6 days ago by • 0
1
vote
1
reply
194
views
Herald: The Biostar Herald for Tuesday, April 23, 2024
herald
updated 4 days ago by 161k • written 4 days ago by 2.7k
0
votes
0
replies
194
views
Job: Ensembl Outreach Project Leader
ebi embl genomics ensembl
5 days ago by Ben_Ensembl ★ 2.4k
6
votes
3
replies
185
views
Interpretting IGV output
IGV
updated 6 days ago by 8.7k • written 6 days ago by ▴ 30
0
votes
2
replies
184
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq edgeR
22 hours ago by Guille • 0
0
votes
2
replies
181
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK BQSR
5 days ago by sainavyav22 • 0
0
votes
1
reply
177
views
homology modelling using swiss model
homology-modeling swiss-model
updated 6 days ago by 6.4k • written 6 days ago by • 0
0
votes
1
reply
172
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing housekeeping Single-cell normalization
updated 2 days ago by 82k • written 2 days ago by • 0
1
vote
1
reply
171
views
Failed kmer content
kmer illumina ngs
updated 4 days ago by 43k • written 5 days ago by • 0
0
votes
1
reply
164
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs methylkit
updated 4 days ago by 141k • written 4 days ago by ▴ 20
0
votes
0
replies
162
views
Forum: Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation scRNA llm
5 days ago by yxwucq • 0
1
vote
1
reply
161
views
WGCNA preservation analysis
WGCNA preservation
updated 4 days ago by 54k • written 4 days ago by ▴ 180
0
votes
1
reply
159
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 4 days ago by ★ 2.4k • written 4 days ago by • 0
0
votes
0
replies
157
views
Job: CTO/founding engineer role at Voyant Bio
engineer
2 days ago by Assaf • 0
0
votes
1
reply
156
views
RNA-seq bacteria contamination
RNA-seq
updated 5 days ago by 141k • written 5 days ago by • 0
1
vote
1
reply
152
views
Including plasmid in transcriptome assemblies
Bacteria BOWTIE2 Transcriptomics STAR
updated 4 days ago by 141k • written 4 days ago by • 0
0
votes
1
reply
152
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 4 days ago by ★ 27k • written 4 days ago by • 0
0
votes
1
reply
150
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray Limma Agilent
updated 1 day ago by ★ 7.0k • written 1 day ago by ▴ 10
0
votes
0
replies
149
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes vcf phasing
1 day ago by HarperReed • 0
0
votes
1
reply
148
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate GEMMA GWAS
updated 3 days ago by • 0 • written 3 days ago by • 0
0
votes
1
reply
147
views
Identification of Transgene insertion sites
Transgene Whole-Genome-Sequencing transgene-sites
updated 5 days ago by 43k • written 5 days ago by • 0
0
votes
1
reply
145
views
Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 4 days ago by ★ 2.4k • written 4 days ago by ▴ 110
1
vote
0
replies
144
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds kaks VCF
2 days ago by rohitsatyam102 ▴ 850
3
votes
0
replies
144
views
News: Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy Generative-AI scRNA Machine-Learning
updated 1 day ago by 43k • written 1 day ago by ▴ 60
0
votes
0
replies
143
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein pdb alpha-carbon
3 days ago by 4fzcgueyp5 • 0
0
votes
0
replies
140
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 6 days ago by 43k • written 7 days ago by • 0
0
votes
0
replies
139
views
Why not use iBAQ for calculating differential abundance of proteins?
protein maxquant
2 days ago by Aspire ▴ 300
0
votes
1
reply
138
views
Plots for DNA methylation data
plots DNA methylation
updated 4 days ago by 141k • written 5 days ago by ▴ 10
0
votes
1
reply
137
views
tbtool
tbtool
updated 5 days ago by 43k • written 5 days ago by • 0
1
vote
1
reply
137
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma voom R
updated 1 day ago by ★ 7.0k • written 1 day ago by ▴ 10
0
votes
0
replies
137
views
Sequence BLAST in plus/minus and plus/plus
blast CRISPR strand sequencing
3 days ago by salias • 0
0
votes
1
reply
136
views
FAM FILE
file Fam
5 days ago by Eleonora • 0
0
votes
0
replies
136
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
2 days ago by avocado123 • 0
0
votes
0
replies
134
views
How to visualize/predict the final transcript from Delly output?
WGS DELLY
2 days ago by simplitia ▴ 130
0
votes
0
replies
133
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA GDCprepare
updated 3 days ago by 43k • written 3 days ago by • 0
0
votes
0
replies
132
views
News: upcoming online statistical courses
Statistics R Data-Analysis
updated 6 days ago by 43k • written 7 days ago by ★ 2.5k
0
votes
0
replies
132
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 6 days ago by 8.7k • written 6 days ago by • 0
0
votes
0
replies
130
views
Job: Ensembl Plants Senior Bioinformatician
ebi embl genomics ensembl
5 days ago by Ben_Ensembl ★ 2.4k
0
votes
1
reply
129
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq nucleosome fragment
updated 5 days ago by 82k • written 5 days ago by • 0
0
votes
0
replies
129
views
News: Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis Statistics R
updated 2 days ago by 43k • written 2 days ago by ★ 2.5k
0
votes
0
replies
127
views
how to read graph_test output of monocle 3
monocle3
2 days ago by synat.keam ▴ 100
0
votes
0
replies
125
views
How to calculate correlation coefficient for chipseq?
chipseq bigwigsummary correlation
2 days ago by Emily ▴ 10
184 results • Page 3 of 4
Recent Votes
A: Deeptools plotHeatmap - Maintain Order of Input BED file
Comment: NGS forensics: how to know if data is fabricated
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Answer: DNA methylation preprocessing
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
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Recent Replies
Comment: gvcf joint calling by zihanss • 0
Thanks for your comment, I get it now.
Answer: ChIP-seq datasets: input samples omitted? by ATpoint 82k
In my hands (and from what I know based on many years here) inputs are almost exclusively used during peak calling to correct for loci-spec…
Comment: How to assign cell types after integration in scRNA by ATpoint 82k
No difference here. After all you typically want a label per cluster/group, so either subset to the control condition to do the assignment,…
Comment: Differential Expression using Isoseq-supplemented reference transcriptome by gaoanwei • 0
I found the question and ASK the GPT4 turbo
Answer: Differential Expression using Isoseq-supplemented reference transcriptome by gaoanwei • 0
Your approach seems reasonable and well-informed, though it's perhaps less customary in the field, which could be why you haven't found pap…
Answer: How many reads for WGS Sequencing? by Mensur Dlakic ★ 27k
It takes 29 seconds to assemble this genome (20 CPUs) with the following statistics: 135 contigs, total 2821177 bp, min 200 bp, max …
Comment: NGS forensics: how to know if data is fabricated by noodle ▴ 520
IMO (and unfortunately) there needs to be an effort to develop these algorithms.
Comment: gvcf joint calling by Jeremy Leipzig 22k
the samples that are `./.` have no coverage (or not enough to call a genotype) and the `0/0` are homozygous reference
Answer: How many reads for WGS Sequencing? by GenoMax 141k
Did you download the complete dataset available from ENA/NCBI SRA? This is an older dataset (from 2012) with a total of 1146212 reads and 1…
Comment: When to use .vcf or .gvcf files from GATK HaplotypeCaller? by zihanss • 0
Hello, I want to know that why my gVCF files have "./." besides "0/0", "1/1"? Thanks
Comment: gvcf joint calling by zihanss • 0
![enter image description here][1] [1]: /media/images/15eedc1a-b2c6-4966-be39-b5173dab And I confused with the file that has "./." and…
Comment: gvcf joint calling by zihanss • 0
![enter image description here][1] [1]: /media/images/16fd502c-4e01-4f56-8562-0e0d4aac Okay, this is the merged gVCF file.
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC: by Mensur Dlakic ★ 27k
Enzymes under the umbrella of `1.1.1.-` work `with NAD(+) or NADP(+) as acceptor`. That only tells you about their cofactors, but not about…
Comment: NGS forensics: how to know if data is fabricated by dsull ★ 5.9k
I don't think people have undertaken the effort to create an anomaly detector for RNAseq -- people's efforts are dedicated towards developi…
Comment: NGS forensics: how to know if data is fabricated by dsull ★ 5.9k
I'd say post on pubpeer -- it's the best forum for this sort of discussion. As for what additional analysis I recommend: I'd say look at s…
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