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189 results • Page 3 of 4
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160
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Forum: Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation scRNA llm
3 days ago by yxwucq • 0
0
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0
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86
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How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy Copy-number-analysis R
updated 3 days ago by 43k • written 3 days ago by • 0
0
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6
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306
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How to slice a gvcf file with tabix?
Tabix bed gvcf
2 days ago by Sd • 0
0
votes
2
replies
175
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Help with Base quality Score Recalibration (BQSR) using GATK
GATK BQSR
3 days ago by sainavyav22 • 0
0
votes
1
reply
143
views
Identification of Transgene insertion sites
Transgene Whole-Genome-Sequencing transgene-sites
updated 3 days ago by 43k • written 3 days ago by • 0
0
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8
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311
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Error in cnetplot enrichplot package
R
updated 3 days ago by 43k • written 3 days ago by • 0
3
votes
9
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419
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 2 days ago by 100k • written 3 days ago by • 0
0
votes
0
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108
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment Genomics Ka-Ks
updated 3 days ago by 43k • written 3 days ago by ▴ 200
3
votes
3
replies
193
views
Genbank vs SRA
ncbi genbank genomics sra
updated 3 days ago by ★ 27k • written 3 days ago by ▴ 520
0
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0
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92
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Analysis of the gene family of a genome.
Genome gene-family
updated 3 days ago by 43k • written 3 days ago by ▴ 80
0
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0
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94
views
File with NCBI summary or Uniprot description
annotation visualisation NCBI Uniprot RNA
updated 3 days ago by 43k • written 3 days ago by • 0
0
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0
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197
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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 43k • written 3 days ago by ▴ 10
1
vote
3
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2.5k
views
Problem to remove subset of patients with plink
plink PED
updated 3 days ago by 10k • written 6.1 years ago by ▴ 10
2
votes
3
replies
196
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from row count to tpm
tpm row-count normalization
3 days ago by michelafrancesconi9 ▴ 20
1
vote
5
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267
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Downsampling fastq file
downsample fastq
updated 4 days ago by 43k • written 4 days ago by ▴ 80
2
votes
3
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318
views
How to establish haplotype-specific gene expression levels
RNA-seq Haplotype
updated 3 hours ago by ★ 5.8k • written 17 days ago by ▴ 60
0
votes
1
reply
130
views
tbtool
tbtool
updated 4 days ago by 43k • written 4 days ago by • 0
0
votes
7
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239
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 53 minutes ago by 141k • written 4 days ago by • 0
3
votes
3
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218
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide Genomic Sequence Uniprot Proteins
updated 4 days ago by 141k • written 4 days ago by ▴ 10
0
votes
1
reply
124
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq nucleosome fragment
updated 4 days ago by 82k • written 4 days ago by • 0
0
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0
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85
views
Help with finding conferences in immuno-informatics/virology
virology conferences immunology
4 days ago by manaswwm ▴ 490
3
votes
3
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717
views
KissDE and batch effect
kissDE kissplice
4 days ago by david.b.rombaut ▴ 10
0
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0
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75
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Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
3 days ago by alifafiq1 • 0
76
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72
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19k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
1 day ago by Kevin Blighe 87k
0
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0
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82
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How to get somatic variation based on RNA-seq data?
RNA-seq variation somatic
4 days ago by feather-W • 0
2
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4
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265
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interpretartion of a vcf file
calling genotype ONT variant diploid
2 days ago by samuelkalandarov2002 ▴ 10
0
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0
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81
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Annotating single cell data automatically
cell annotation single
4 days ago by Gerard • 0
0
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0
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82
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News: Online course: DNA methylation
Pacbio Nanopore DnaMethylation Evolution
4 days ago by carlopecoraro2 ★ 2.5k
0
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0
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125
views
Job: Ensembl Plants Senior Bioinformatician
ebi embl genomics ensembl
4 days ago by Ben_Ensembl ★ 2.4k
2
votes
4
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296
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What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
2 days ago by HyperEvo • 0
0
votes
1
reply
149
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RNA-seq bacteria contamination
RNA-seq
updated 4 days ago by 141k • written 4 days ago by • 0
0
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2
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192
views
Result of running of p3_in.pl
primer3
updated 4 days ago by 141k • written 4 days ago by • 0
0
votes
1
reply
131
views
FAM FILE
file Fam
4 days ago by Eleonora • 0
0
votes
0
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73
views
Imputation advice
imputation
4 days ago by kl ▴ 10
3
votes
5
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263
views
Per base sequence content error in RNAseq analysis
RNA-seq analysis
updated 4 days ago by 141k • written 4 days ago by • 0
0
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0
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90
views
Trimming best practices for SNP calling
trimming SNP trimmomatic
4 days ago by Enrique • 0
3
votes
5
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544
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
4 days ago by n_navy • 0
0
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0
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73
views
Correct way of reducing predictive model complexity
lasso glmnet predictvemodeling regression
4 days ago by sativus ▴ 20
6
votes
3
replies
179
views
Interpretting IGV output
IGV
updated 4 days ago by 8.7k • written 4 days ago by ▴ 30
0
votes
1
reply
174
views
homology modelling using swiss model
homology-modeling swiss-model
updated 4 days ago by 6.4k • written 5 days ago by • 0
0
votes
0
replies
81
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER MARINA ARACNe
4 days ago by Biostars2200 • 0
1
vote
5
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318
views
DYH17 Structure Prediction
BLAST Protein-Structure-Prediction
3 days ago by anasjamshed ▴ 120
0
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0
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125
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 4 days ago by 8.7k • written 4 days ago by • 0
3
votes
2
replies
271
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni R Statistics p-value Fisher
4 days ago by kristiewyleung • 0
2
votes
5
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450
views
Marking duplicates using UMIs
Deduplication UMI
updated 4 days ago by 19k • written 5 days ago by • 0
0
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0
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138
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 5 days ago by 43k • written 5 days ago by • 0
0
votes
0
replies
138
views
Bacterial genome alignment with mauve
Bacteria mauve genome
5 days ago by rthapa ▴ 90
0
votes
0
replies
133
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation CGenFF Gromacs VMD
5 days ago by Mamatha Y S • 0
0
votes
0
replies
130
views
News: upcoming online statistical courses
Statistics R Data-Analysis
updated 5 days ago by 43k • written 5 days ago by ★ 2.5k
0
votes
4
replies
523
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq gene-expression
updated 5 days ago by 82k • written 6 days ago by ▴ 140
189 results • Page 3 of 4
Recent Votes
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
A: How to process (seems) Agilent microarrry data?
Comment: genome assembly records not present in assembly_summary.txt
Answer: genome assembly records not present in assembly_summary.txt
Answer: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
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Recent Replies
Comment: Low mapping rate with Salmon by i.sudbery 19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
Comment: genome assembly records not present in assembly_summary.txt by sapuizait ▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question by bk11 ★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon by GenoMax 141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely aligning in regions wh…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File? by cmdcolin ★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon by Patadu94 • 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon by Patadu94 • 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq by pinheirofabiano ▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
Comment: Low mapping rate with Salmon by Patadu94 • 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
Answer: Create a new bed file with all pairwise combinations between two other bed files by Pierre Lindenbaum 161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t%d\…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J • 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question by starswillfade ▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question by starswillfade ▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Answer: genome assembly records not present in assembly_summary.txt by GenoMax 141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
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