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438 results • Page 3 of 9
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0
votes
0
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177
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RNA-seq: full length gene
RNA-seq
updated 10 days ago by 43k • written 10 days ago by • 0
0
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0
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160
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Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly phased Haplotype Annotation
10 days ago by turcoa1 • 0
0
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0
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172
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Designing single-stable RNA molecules
structure RNA
10 days ago by Edna • 0
0
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0
replies
184
views
How to visualize/predict the final transcript from Delly output?
WGS DELLY
10 days ago by simplitia ▴ 130
1
vote
1
reply
244
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Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing housekeeping Single-cell normalization
updated 10 days ago by 82k • written 10 days ago by • 0
0
votes
0
replies
165
views
How to calculate correlation coefficient for chipseq?
chipseq bigwigsummary correlation
11 days ago by Emily ▴ 10
1
vote
0
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181
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds kaks VCF
11 days ago by rohitsatyam102 ▴ 850
0
votes
0
replies
162
views
how to read graph_test output of monocle 3
monocle3
11 days ago by synat.keam ▴ 100
0
votes
1
reply
513
views
GAPIT p-value significance threshold
GAPIT p-value GWAS
updated 11 days ago by • 0 • written 5 months ago by • 0
0
votes
0
replies
160
views
Why not use iBAQ for calculating differential abundance of proteins?
protein maxquant
11 days ago by Aspire ▴ 330
0
votes
3
replies
328
views
Highest variable features in single cell data
single-cell
updated 9 days ago by ★ 2.4k • written 11 days ago by ▴ 30
1
vote
3
replies
402
views
PCA plot
DESeq2 PCAplot
updated 7 days ago by 4.2k • written 11 days ago by ▴ 10
0
votes
0
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158
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein pdb alpha-carbon
11 days ago by 4fzcgueyp5 • 0
0
votes
2
replies
288
views
Annovar using R package
Annovar gnomAD R
10 days ago by DKA ▴ 40
0
votes
5
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406
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Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 11 days ago by 142k • written 12 days ago by ▴ 90
0
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0
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156
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA GDCprepare
updated 11 days ago by 43k • written 12 days ago by • 0
0
votes
0
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318
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome PGAP NCBI roary Prokka
12 days ago by pramach1 ▴ 40
0
votes
1
reply
187
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate GEMMA GWAS
updated 12 days ago by • 0 • written 12 days ago by • 0
0
votes
0
replies
157
views
Sequence BLAST in plus/minus and plus/plus
blast CRISPR strand sequencing
12 days ago by salias • 0
0
votes
5
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406
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
updated 9 days ago by 100k • written 12 days ago by ▴ 10
0
votes
0
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134
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq single-cell suppa alternative-splicing
updated 11 days ago by 43k • written 12 days ago by • 0
1
vote
2
replies
266
views
alignment result
RNA-seq samtools hisat2
11 days ago by ahmad.sajad4541 • 0
0
votes
0
replies
128
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
12 days ago by Kash ▴ 110
0
votes
1
reply
177
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 12 days ago by ★ 27k • written 12 days ago by • 0
2
votes
2
replies
316
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 11 days ago by 43k • written 12 days ago by ▴ 140
2
votes
9
replies
910
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 12 days ago by 4.2k • written 6 months ago by • 0
0
votes
11
replies
643
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
10 days ago by atowns21 • 0
0
votes
1
reply
189
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 12 days ago by ★ 2.4k • written 12 days ago by • 0
0
votes
0
replies
110
views
The concept of co-occurrence network structure
co-occurence microbiome network
13 days ago by ohtang7 ▴ 40
0
votes
1
reply
187
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs methylkit
updated 13 days ago by 142k • written 13 days ago by ▴ 20
0
votes
5
replies
384
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
12 days ago by njornet ▴ 20
0
votes
0
replies
112
views
Software to calculate RSCU, ENC other than codonw
rscu codonw
updated 13 days ago by 43k • written 13 days ago by • 0
0
votes
0
replies
114
views
Merging replicates from Encode project
CHIP-seq encode
13 days ago by Nurken • 0
1
vote
3
replies
272
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
13 days ago by WouterDeCoster 47k
1
vote
3
replies
313
views
some error in building kraken2 database
metagenome kraken2
12 days ago by Art1ess • 0
0
votes
1
reply
184
views
Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 13 days ago by ★ 2.4k • written 13 days ago by ▴ 110
1
vote
1
reply
199
views
Failed kmer content
kmer illumina ngs
updated 13 days ago by 43k • written 13 days ago by • 0
0
votes
0
replies
103
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy Copy-number-analysis R
updated 13 days ago by 43k • written 13 days ago by • 0
0
votes
1
reply
165
views
Identification of Transgene insertion sites
Transgene Whole-Genome-Sequencing transgene-sites
updated 13 days ago by 43k • written 13 days ago by • 0
0
votes
8
replies
403
views
Error in cnetplot enrichplot package
R
updated 13 days ago by 43k • written 13 days ago by • 0
0
votes
0
replies
119
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment Genomics Ka-Ks
updated 13 days ago by 43k • written 13 days ago by ▴ 200
0
votes
0
replies
105
views
Analysis of the gene family of a genome.
Genome gene-family
updated 13 days ago by 43k • written 13 days ago by ▴ 80
0
votes
0
replies
108
views
File with NCBI summary or Uniprot description
annotation visualisation NCBI Uniprot RNA
updated 13 days ago by 43k • written 13 days ago by • 0
0
votes
0
replies
213
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS Meta-analysis
updated 13 days ago by 43k • written 13 days ago by ▴ 10
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink PED
updated 13 days ago by 10k • written 6.2 years ago by ▴ 10
1
vote
8
replies
479
views
Downsampling fastq file
downsample fastq
5 days ago by marco.barr ▴ 90
0
votes
1
reply
151
views
tbtool
tbtool
updated 14 days ago by 43k • written 14 days ago by • 0
0
votes
10
replies
530
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 6 days ago by 19k • written 14 days ago by • 0
0
votes
1
reply
144
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq nucleosome fragment
updated 14 days ago by 82k • written 14 days ago by • 0
0
votes
0
replies
98
views
Help with finding conferences in immuno-informatics/virology
virology conferences immunology
14 days ago by manaswwm ▴ 510
438 results • Page 3 of 9
Recent Votes
Comment: High Malat-1 expression in single cell data
A: Meme-Tools: Bit score
Meme-Tools: Bit score
Meme-Tools: Bit score
Comment: error in R code
DEXSeq multiple time points
How to find the most frequent alternative-splicing event from DEXSEQ data?
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Popular Question to bhumm ▴ 140
Teacher to Matthias Zepper 4.6k
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Recent Replies
Answer: Gene ontology and homologs by geneontologyhelp ▴ 390
No. Homology is defined as shared common ancestry. Two genes that take part in the same biological process may not have the same functio…
Answer: error in R code by Matthias Zepper 4.6k
I quickly googled [the source code of that function][1], and the error is triggered by this condition: if(length(wn) < 1 || !is.whol…
Comment: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read by kalavattam ▴ 190
Thanks for the explanation. I noticed and corrected a typo in which "*read* reverse strand" initially read as "*mate* reverse strand" in t…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by sovrappensiero ▴ 90
It's a commercial product, a *Staphylococcus hominis* genome. This species is not found in the DADA2 results, so I guess DADA2 is not ident…
Comment: Question regarding WGCNA by Ram 43k
Plots are incomplete without legends. Please share the complete plot with mappings for shape and color.
Comment: Quetion regarding WGCNA by deepak • 0
Thank you for your reply andres.firrincieli. I have attached the PCA plot of the expression data used in the WGCNA. ![enter imag…
Comment: Design matrix Differential expression analysis by SHN ▴ 40
Got it, thank you for your response. SN
Comment: How to interpret DEXseq results in therms of significance by Sara ▴ 30
Hi, I used write.table(as.data.frame(DEXSeqResults(MyObj)), "Results.tsv", quote=FALSE, sep="\t", dec=".") to save the result but I recei…
Comment: Tissue-specific DEG analysis with DEseq2 by M. ▴ 30
Can I ask what do you exactly mean by same experiment? If you are talking about the same donor and the same procedure, unfortunately, not a…
Comment: install package: package ‘gmwm’ is not available for this version of R by Ram 43k
Find someone with computer skills near you and consult them. From your posts on the forum, it's clear that you need help at a level that we…
Comment: Gene Specific coverage from WGS data by GenoMax 142k
This is not going to work no matter what program you use since the chromosome identifiers in your GTF (`MN908947.3 `) do not match your BA…
Comment: install.packages("imudata") - package ‘imudata’ is not available for this versio by Ram 43k
Read the answers in the post, understand them and try to implement them.
Comment: High Malat-1 expression in single cell data by t.montserrat.ayuso ▴ 10
Just using the normalized expression of Malat1 works.
Comment: Can I merge Hi-C fastq files from different lanes? by Winter • 0
Awesome, thank you for the concise and straight-forward answer!
Comment: error in R code by ATpoint 82k
Look, before you keep posting these sorts of questions and might gross of users, please read and follow https://www.biostars.org/p/357878/ …
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