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85 results • Page 1 of 2
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0
votes
0
replies
16
views
ChIP-seq datasets: input samples omitted?
ChIP-seq Normalization NGS
updated 40 minutes ago by 43k • written 1 hour ago by ▴ 40
0
votes
0
replies
19
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray Limma Agilent
2 hours ago by hagl ▴ 10
0
votes
0
replies
70
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes vcf phasing
7 hours ago by HarperReed • 0
1
vote
0
replies
50
views
Simulation of label-free bottom-up proteomics expression dataset
label-free bottom-up lc-ms proteomics
10 hours ago by KABILAN ▴ 50
0
votes
0
replies
49
views
Running Phylogenetic Analysis With NCBI Genome
population genetics phylogenetic species sequencing
10 hours ago by SineWave • 0
0
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0
replies
51
views
RNA-seq: full length gene
RNA-seq
updated 40 minutes ago by 43k • written 11 hours ago by • 0
0
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0
replies
46
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly phased Haplotype Annotation
12 hours ago by turcoa1 • 0
0
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0
replies
63
views
Designing single-stable RNA molecules
structure RNA
19 hours ago by Edna • 0
0
votes
0
replies
75
views
How to visualize/predict the final transcript from Delly output?
WGS DELLY
19 hours ago by simplitia ▴ 130
0
votes
1
reply
112
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing housekeeping Single-cell normalization
updated 21 hours ago by 82k • written 21 hours ago by • 0
0
votes
0
replies
79
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
23 hours ago by avocado123 • 0
0
votes
0
replies
67
views
How to calculate correlation coefficient for chipseq?
chipseq bigwigsummary correlation
1 day ago by Emily ▴ 10
1
vote
0
replies
86
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds kaks VCF
1 day ago by rohitsatyam102 ▴ 850
0
votes
0
replies
72
views
how to read graph_test output of monocle 3
monocle3
1 day ago by synat.keam ▴ 100
0
votes
1
reply
403
views
GAPIT p-value significance threshold
GAPIT p-value GWAS
updated 1 day ago by • 0 • written 4 months ago by • 0
0
votes
0
replies
85
views
Why not use iBAQ for calculating differential abundance of proteins?
protein maxquant
1 day ago by Aspire ▴ 300
0
votes
2
replies
167
views
Highest variable features in single cell data
single-cell
updated 20 hours ago by 43k • written 1 day ago by • 0
0
votes
2
replies
203
views
PCA plot
DESeq2 PCAplot
updated 7 hours ago by 82k • written 1 day ago by ▴ 10
0
votes
0
replies
110
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein pdb alpha-carbon
1 day ago by 4fzcgueyp5 • 0
0
votes
2
replies
217
views
Annovar using R package
Annovar gnomAD R
20 hours ago by DKA ▴ 40
0
votes
5
replies
291
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 1 day ago by 141k • written 2 days ago by ▴ 90
0
votes
0
replies
130
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA GDCprepare
updated 1 day ago by 43k • written 2 days ago by • 0
0
votes
0
replies
255
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome PGAP NCBI roary Prokka
2 days ago by pramach1 ▴ 40
0
votes
1
reply
141
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate GEMMA GWAS
updated 2 days ago by • 0 • written 2 days ago by • 0
0
votes
0
replies
131
views
Sequence BLAST in plus/minus and plus/plus
blast CRISPR strand sequencing
2 days ago by salias • 0
0
votes
4
replies
250
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
1 day ago by sehriban.buyukkilic ▴ 10
0
votes
0
replies
112
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq single-cell suppa alternative-splicing
updated 1 day ago by 43k • written 2 days ago by • 0
1
vote
2
replies
200
views
alignment result
RNA-seq samtools hisat2
1 day ago by ahmad.sajad4541 • 0
0
votes
0
replies
94
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet DoubletFinder Seurat modelHomotypic
updated 1 day ago by 43k • written 2 days ago by • 0
0
votes
0
replies
104
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
2 days ago by Kash ▴ 110
0
votes
1
reply
145
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 2 days ago by ★ 27k • written 2 days ago by • 0
0
votes
2
replies
237
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 1 day ago by 43k • written 2 days ago by ▴ 140
2
votes
9
replies
821
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 2 days ago by 4.2k • written 6 months ago by • 0
0
votes
11
replies
473
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
17 hours ago by atowns21 • 0
0
votes
1
reply
150
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 2 days ago by ★ 2.4k • written 2 days ago by • 0
0
votes
0
replies
94
views
The concept of co-occurrence network structure
co-occurence microbiome network
3 days ago by ohtang7 ▴ 40
0
votes
1
reply
156
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs methylkit
updated 3 days ago by 141k • written 3 days ago by ▴ 20
0
votes
5
replies
290
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
2 days ago by njornet ▴ 20
0
votes
0
replies
88
views
Software to calculate RSCU, ENC other than codonw
rscu codonw
updated 3 days ago by 43k • written 3 days ago by • 0
0
votes
0
replies
96
views
Merging replicates from Encode project
CHIP-seq encode
3 days ago by Nurken • 0
1
vote
3
replies
209
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
3 days ago by WouterDeCoster 47k
1
vote
3
replies
250
views
some error in building kraken2 database
metagenome kraken2
2 days ago by Art1ess • 0
0
votes
1
reply
132
views
Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 3 days ago by ★ 2.4k • written 3 days ago by ▴ 110
1
vote
1
reply
167
views
Failed kmer content
kmer illumina ngs
updated 3 days ago by 43k • written 3 days ago by • 0
0
votes
0
replies
86
views
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
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
votes
8
replies
311
views
Error in cnetplot enrichplot package
R
updated 3 days ago by 43k • written 3 days ago by • 0
0
votes
0
replies
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
0
votes
0
replies
92
views
Analysis of the gene family of a genome.
Genome gene-family
updated 3 days ago by 43k • written 3 days ago by ▴ 80
0
votes
0
replies
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
85 results • Page 1 of 2
Recent Votes
Answer: genome assembly records not present in assembly_summary.txt
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)
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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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