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1,000 results • Page 5 of 20
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107
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How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq DEXSeqDataSet SGSeq
20 days ago by Sara ▴ 30
0
votes
2
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204
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Longitudinal analysis of subpopulations: which approach is better?
differential-expression DEG model
20 days ago by Lluís R. ★ 1.2k
0
votes
0
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127
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Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics Mass-spectrometry Proteins
updated 5 days ago by 43k • written 20 days ago by ▴ 40
0
votes
2
replies
250
views
What should I consider as FASTA for dataset?
PDB FASTA
19 days ago by Nafi • 0
0
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0
replies
612
views
Differential accessibility using DiffBinf
diffbind
20 days ago by Shloka • 0
0
votes
0
replies
119
views
vg call vs vg surject
vg variation graphs
updated 20 days ago by 142k • written 20 days ago by • 0
0
votes
1
reply
246
views
Finding batch and outlayers
Pca
updated 20 days ago by ▴ 460 • written 20 days ago by • 0
2
votes
2
replies
246
views
PDB related issue
rcsb pdb
updated 20 days ago by ▴ 580 • written 20 days ago by • 0
0
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9
replies
2.6k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome base-calling fastq nanopore
updated 20 days ago by 43k • written 9 months ago by • 0
1
vote
2
replies
288
views
Downloading full alignments from Pfam
pfam
14 days ago by bef1 • 0
0
votes
0
replies
142
views
adjusting for confounders in LMER in R
confounders LMER R
updated 20 days ago by 14k • written 21 days ago by ▴ 20
1
vote
3
replies
384
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 21 days ago by 82k • written 21 days ago by ▴ 10
0
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0
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159
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STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
21 days ago by tnminh89 ▴ 10
0
votes
0
replies
160
views
Filter low express genes in microarray data
microarray
22 days ago by Chris ▴ 280
0
votes
0
replies
587
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell Spatial-Transcriptomics
22 days ago by biocellbio • 0
0
votes
0
replies
226
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes vcf phasing
23 days ago by HarperReed • 0
1
vote
0
replies
176
views
Simulation of label-free bottom-up proteomics expression dataset
label-free bottom-up lc-ms proteomics
23 days ago by KABILAN ▴ 70
0
votes
0
replies
191
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics phylogenetic
updated 22 days ago by 43k • written 23 days ago by • 0
0
votes
0
replies
192
views
RNA-seq: full length gene
RNA-seq
updated 23 days ago by 43k • written 23 days ago by • 0
0
votes
0
replies
173
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly phased Haplotype Annotation
23 days ago by turcoa1 • 0
0
votes
0
replies
185
views
Designing single-stable RNA molecules
structure RNA
23 days ago by Edna • 0
0
votes
0
replies
198
views
How to visualize/predict the final transcript from Delly output?
WGS DELLY
23 days ago by simplitia ▴ 130
1
vote
1
reply
270
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing housekeeping Single-cell normalization
updated 24 days ago by 82k • written 24 days ago by • 0
0
votes
0
replies
183
views
How to calculate correlation coefficient for chipseq?
chipseq bigwigsummary deeptools correlation
5 days ago by Emily ▴ 20
1
vote
0
replies
197
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds kaks VCF
24 days ago by rohitsatyam102 ▴ 870
0
votes
0
replies
174
views
how to read graph_test output of monocle 3
monocle3
24 days ago by synat.keam ▴ 100
0
votes
1
reply
537
views
GAPIT p-value significance threshold
GAPIT p-value GWAS
updated 24 days ago by • 0 • written 5 months ago by • 0
0
votes
0
replies
179
views
Why not use iBAQ for calculating differential abundance of proteins?
protein maxquant
24 days ago by Aspire ▴ 330
0
votes
4
replies
428
views
Highest variable features in single cell data
single-cell
12 days ago by carolofharvest ▴ 40
1
vote
3
replies
455
views
PCA plot
DESeq2 PCAplot
updated 21 days ago by 4.2k • written 24 days ago by ▴ 10
0
votes
0
replies
175
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein pdb alpha-carbon
24 days ago by 4fzcgueyp5 • 0
0
votes
2
replies
315
views
Annovar using R package
Annovar gnomAD R
23 days ago by DKA ▴ 40
0
votes
5
replies
446
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 24 days ago by 142k • written 25 days ago by ▴ 90
0
votes
0
replies
172
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA GDCprepare
updated 25 days ago by 43k • written 25 days ago by • 0
0
votes
0
replies
331
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome PGAP NCBI roary Prokka
25 days ago by pramach1 ▴ 40
0
votes
1
reply
211
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate GEMMA GWAS
updated 25 days ago by • 0 • written 25 days ago by • 0
0
votes
0
replies
170
views
Sequence BLAST in plus/minus and plus/plus
blast CRISPR strand sequencing
25 days ago by salias • 0
0
votes
5
replies
468
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
updated 22 days ago by 100k • written 25 days ago by ▴ 10
0
votes
0
replies
147
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq single-cell suppa alternative-splicing
updated 25 days ago by 43k • written 25 days ago by • 0
1
vote
2
replies
284
views
alignment result
RNA-seq samtools hisat2
24 days ago by ahmad.sajad4541 • 0
0
votes
0
replies
141
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
25 days ago by Kash ▴ 110
0
votes
1
reply
192
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 25 days ago by ★ 27k • written 25 days ago by • 0
2
votes
2
replies
339
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 25 days ago by 43k • written 25 days ago by ▴ 140
2
votes
9
replies
944
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 25 days ago by 4.2k • written 7 months ago by • 0
0
votes
11
replies
721
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
23 days ago by atowns21 • 0
0
votes
1
reply
215
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 26 days ago by ★ 2.5k • written 26 days ago by • 0
0
votes
0
replies
122
views
The concept of co-occurrence network structure
co-occurence microbiome network
26 days ago by ohtang7 ▴ 40
0
votes
1
reply
210
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs methylkit
updated 26 days ago by 142k • written 26 days ago by ▴ 20
0
votes
5
replies
434
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
25 days ago by njornet ▴ 20
0
votes
0
replies
127
views
Software to calculate RSCU, ENC other than codonw
rscu codonw
updated 26 days ago by 43k • written 26 days ago by • 0
1,000 results • Page 5 of 20
Recent Votes
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: How to add Ensembl id to cluster.markers in Seurat
How to add Ensembl id to cluster.markers in Seurat
Comment: Duplicated sequence samtools
Answer: Duplicated sequence samtools
Answer: Duplicated sequence samtools
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Recent Awards • All
Scholar to Pierre Lindenbaum 161k
Voter to Sara ▴ 30
Popular Question to carlopecoraro2 ★ 2.5k
Popular Question to scideas ▴ 30
Popular Question to Muhammad • 0
Popular Question to synat.keam ▴ 100
Scholar to jv ★ 1.8k
Recent Replies
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by Pierre Lindenbaum 161k
> Cannot read non-existent file: file:///local/home/User/VCF_Filtering/biostar.code your file doesn't exist, is at the wrong place etc.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by ajbarrett98 • 0
Hi Pierre, I am attempting to run this code and am running into this error: (jvar) $ jvarkit vcffilterjdk -f biostar.code Dart_VCF2_Or…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by ATpoint 82k
I cannot give a precise answer, as ML is not my field, but generally, why don't you apply the method to pseudobulks of the exact single-cel…
Answer: geom_bar issue in ggplot2 with xlim() by ATpoint 82k
https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim
Comment: What marks a De-Novo Genome assembly as FAILED? by Umer ▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
Comment: HGVS Nomenclature of Multiple Indels found in Cis by LauferVA 4.2k
how has this code progressed? is it publically available? would you want to work together?
Comment: Design for complex RNA-Seq experiment using Deseq2 by Ezequiel • 0
I completely agree with most points. The PCA shows that the biggest driver of difference is the patients themselves, with PRE and POST time…
Comment: Add stats to the plot by marco.barr ▴ 130
Hi, you can add statistical annotations using `ggpubr` function `stat_pvalue_manual `. You need to make sure you calculate the p-values fir…
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from by ATpoint 82k
Use everything before the whitespace in list.txt, for example `A00869:294:HCW57DSXY:2:1101:3929:1000` and not `A00869:294:HCW57DSXY:2:1101:…
Answer: CellRanger output more cells than specified using --force-cells? Why? by scideas ▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data by Muhammad • 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors) by nguyenn6 • 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed by anton.i.petrov • 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp by analyst ▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
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