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122,008 results • Page 610 of 2441
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0
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917
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CreateSomaticPanelOfNormals
GATK CreateSomaticPanelOfNormals PON
4.2 years ago by jhy ▴ 10
0
votes
0
replies
907
views
Modifying Genbank Contamination File for Bedtools
Genome-Assembly Linux
updated 4.1 years ago by 45k • written 4.2 years ago by ▴ 20
3
votes
6
replies
3.4k
views
how to filter out all the homozygous genotypes in a multi sample VCF file?
vcf
4.2 years ago by Nahid Bandi K • 0
9
votes
7
replies
8.7k
views
Aligning MiSeq targeted amplicons (ultra-deep sequencing)
Targeted-Sequencing MiSeq ultra-deep BWA Alignment
updated 3.8 years ago by 45k • written 11.1 years ago by ▴ 130
0
votes
0
replies
827
views
How do I make bwa-mem and bowtie2 less stringent?
DNA-seq bwa-mem bowtie2
4.2 years ago by gt ▴ 30
0
votes
2
replies
1.5k
views
How to extract reads for HLAscan
HLA genotyping NGS
4.2 years ago by from the mountains ▴ 250
2
votes
1
reply
1.5k
views
How were CCLE SNPs annotated?
annotation CCLE SNP
4.2 years ago by A. Domingues ★ 2.7k
0
votes
2
replies
1.2k
views
inquiry related to rsid
TWAS vcf rsid predixcan
updated 2.6 years ago by 45k • written 4.2 years ago by ▴ 150
1
vote
4
replies
5.0k
views
Sequencing depth with 10x Genomics
10x cell RNA-seq single
updated 4.2 years ago by ★ 19k • written 4.2 years ago by ▴ 10
1
vote
0
replies
803
views
Tool: BIRCH Bioinformatics System v3.80
alignment RNA-seq genome assembly sequence phylogeny
4.2 years ago by brian.fristensky ▴ 460
1
vote
4
replies
1.7k
views
guilt by association
pathways analyses R
4.2 years ago by pinheirofabiano ▴ 130
1
vote
17
replies
4.9k
views
SNP filtering
vcf SNP
updated 2.6 years ago by 45k • written 4.2 years ago by ▴ 150
0
votes
0
replies
780
views
RNA-seq differential expression analysis at specific defined intervals (downstream 1kb adjacent region to repetitive elements)
RNA-seq
4.2 years ago by jennxyzhang • 0
0
votes
0
replies
767
views
Multiome analysis: MAESTRO or Cell Ranger ACR
intergration multiome scRNA-seq scATAC-seq data
4.2 years ago by enh • 0
1
vote
2
replies
1.6k
views
BOLT-LMM error ERROR: 6:63979:C:T has Phased = 2 (not 0)
bgen bolt-lmm
updated 2.4 years ago by 45k • written 4.2 years ago by ▴ 10
0
votes
4
replies
1.4k
views
Microarray Data in R, Annotation of Transcript clusters
RStudio affy microarray
updated 4.2 years ago by 89k • written 4.2 years ago by • 0
1
vote
3
replies
2.6k
views
How to filter VCF by the variant allele depth of a specific sample
bcftools VCF
4.2 years ago by john_campbell1 • 0
0
votes
11
replies
2.7k
views
error in R
RNASeq
updated 4.2 years ago by 45k • written 4.2 years ago by ▴ 10
1
vote
1
reply
2.5k
views
PLINK Error: Too many distinct nonstandard chromosome/contig names.
PLINK
updated 4.2 years ago by 11k • written 4.2 years ago by ▴ 140
0
votes
0
replies
917
views
metascape or STRING
Metascape STRING
4.2 years ago by fionajcunningham • 0
1
vote
2
replies
1.9k
views
Issue with bed to bam conversion - sequence in bam headers
bam bed
updated 4.2 years ago by 154k • written 4.2 years ago by • 0
2
votes
5
replies
6.1k
views
How to get gseKEGG() to accept an input gene list?
clusterprofiler dose gene-enrichment-analysis R
updated 2.6 years ago by ▴ 30 • written 4.2 years ago by ▴ 20
16
votes
15
replies
16k
views
8 follow
BAM files compression
bam
updated 4.2 years ago by ▴ 240 • written 5.7 years ago by ▴ 750
0
votes
4
replies
1.7k
views
variant calling
mutect2
updated 4.2 years ago by ▴ 30 • written 4.2 years ago by • 0
0
votes
0
replies
643
views
rmaps fiel output
RBPs splicing rMATs rmaps
4.2 years ago by Larry • 0
0
votes
4
replies
1.7k
views
"Illegal instruction" error when I use the latest STARsolo to analysis 10X genomics data
statsolo 10x
updated 2.6 years ago by • 0 • written 4.2 years ago by ▴ 80
3
votes
4
replies
2.7k
views
clusterprofiler for comparing differentially expressed genes
clusterProfiler comparecluster
4.2 years ago by najibveto ▴ 130
0
votes
0
replies
727
views
pycoQC Report - Interval unit in output over time plot
QC pycoQC Nanopore
4.2 years ago by chrys ▴ 80
3
votes
2
replies
1.3k
views
How to retrieve total gene numbers per cluster
seurat R
updated 4.2 years ago by ★ 1.7k • written 4.2 years ago by ▴ 30
0
votes
0
replies
1.2k
views
Validation of WES pipeline using NIST7035 and NIST7086 of NA12878
using pipeline validation NA12878 WES data
4.2 years ago by smeeta • 0
2
votes
3
replies
3.0k
views
How to get GTF file of virus genome
genome gene assembly
updated 4.2 years ago by • 0 • written 5.3 years ago by ▴ 170
0
votes
0
replies
1.4k
views
Job: Computational Biologist
research biology nextgen mizzou computational
4.2 years ago by stinsons • 0
0
votes
1
reply
1.1k
views
Expression recursion level exceeded Error in Admixture using mac computer
admixture
4.2 years ago by alexis.diaz • 0
3
votes
2
replies
2.7k
views
Using 'expand' in snakemake target rule with constraints
snakemake glob_wildcards expand
4.2 years ago by cfos4698 ★ 1.2k
3
votes
1
reply
1.2k
views
Bioconductor package specific website
Bioconductor Rstats R
updated 4.2 years ago by ★ 1.2k • written 4.2 years ago by ★ 2.0k
0
votes
0
replies
719
views
Indel frequency analysis from CRISPR modification using sequencing data.
CRISPR Indel Cas9 frequency site cut
4.2 years ago by ms3389 • 0
0
votes
0
replies
873
views
Nebula .cram to .bam via samtools
bam analysis cram samtools
4.2 years ago by christian.palmer • 0
18
votes
3
replies
10k
views
Is There Any Freeware To Analyze Electrophoresis Gels?
analysis software
updated 4.2 years ago by ▴ 10 • written 15.5 years ago by ▴ 150
0
votes
0
replies
896
views
Strelka2 stomatic calls, where is the GT tag ?
strelka annovar variant
4.2 years ago by simplitia ▴ 130
8
votes
2
replies
3.3k
views
How to run vg giraffe for sv genotyping?
vg
updated 4.2 years ago by ▴ 760 • written 4.2 years ago by 24k
0
votes
1
reply
1.0k
views
Identifying novel proteins from bacterial genomes
annotations database bacteria
updated 4.2 years ago by ▴ 590 • written 4.2 years ago by • 0
0
votes
1
reply
1.2k
views
converting genomic version for annovar database?
annovar variant
updated 4.2 years ago by ▴ 580 • written 4.2 years ago by ▴ 130
0
votes
2
replies
4.4k
views
how to merge a subset dataset back to master seurat object
scRNA RNAseq
updated 4.2 years ago by ★ 19k • written 4.2 years ago by ▴ 250
0
votes
0
replies
598
views
Comparative methylation between two isogenic strains of E coli
nanopolish isogenic methylation
4.2 years ago by lkthomp06 • 0
2
votes
5
replies
1.7k
views
How to automatically distinguish single vs. bulk GEO datasets (in ARCHS4 collection or in general) ?
scRNAseq
4.2 years ago by Alexander ▴ 220
0
votes
1
reply
1.0k
views
Parallelize microRNA targets
RNA-Seq
updated 4.2 years ago by 45k • written 4.2 years ago by • 0
2
votes
2
replies
5.0k
views
Recommended PC Hardware for Molecular Dynamics in 2021
PC configuration hardware moleculardynamics
updated 4.2 years ago by ★ 30k • written 4.2 years ago by • 0
4
votes
3
replies
1.4k
views
FeatureCounts dont read all features
featureCounts
updated 4.2 years ago by 154k • written 4.2 years ago by • 0
2
votes
1
reply
907
views
Validate TCGA DEGs with GEOdatabase
DEGs TCGA GEOdatabase
updated 4.2 years ago by 3.3k • written 4.2 years ago by • 0
0
votes
2
replies
1.2k
views
What are the conventions/how to tell what a GSM has had done to it?
GSE GSM methylation minfi GEOquery
updated 4.2 years ago by ▴ 10 • written 4.3 years ago by • 0
122,008 results • Page 610 of 2441
Recent Votes
Answer: DESeq2 on metagenome KO counts
Answer: DESeq2 on metagenome KO counts
Comment: GUI commercial software for 10x single cell gene expression analysis
Answer: GUI commercial software for 10x single cell gene expression analysis
Answer: GUI commercial software for 10x single cell gene expression analysis
Answer: GUI commercial software for 10x single cell gene expression analysis
C: What Does Cds And Exon Mean In A Gtf File?
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Recent Replies
Comment: DESeq2 on metagenome KO counts by ATpoint 89k
Both vst or logcpm will favor expression level (magnitude of counts) rather than differences in a hclust/heatmap. For differences you need …
Comment: DESeq2 on metagenome KO counts by ATpoint 89k
The DESeq2 developer has advised many times against DESeq2 for metagenomics. Please search for related posts over at support.bioconductor.o…
Answer: DESeq2 on metagenome KO counts by andres.firrincieli 3.9k
I wouldn’t use DESeq2 on aggregated raw counts per KO, because doing so means accepting two pretty big assumptions: 1. All genes with t…
Answer: DESeq2 on metagenome KO counts by Aleksandra ▴ 180
(I apologise for my previous reply; I wanted to be as detailed as possible) DESeq2 handles KO counts perfectly well. For a time-series des…
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 180
I apologise for how that sounded; I wanted to be as detailed as possible.
Comment: GUI commercial software for 10x single cell gene expression analysis by Istvan Albert 103k
A comment on: "*Wonky analysis is possible even with open-source R libraries.*" True - and arguably, the risk of a wonky analysis is actua…
Comment: GUI commercial software for 10x single cell gene expression analysis by GenoMax 154k
`Trailmaker` likely only supports Parse's evercode data. <br> `BioTuring` does not appear to have published pricing. <br> `Rosalind` appear…
Answer: GUI commercial software for 10x single cell gene expression analysis by firestar ★ 1.7k
Found a few more when I asked around. I have no idea how good or bad these are. If anyone has used these or knows more about these, feel fr…
Comment: How to handle TrEMBL proteins without gene annotation in plasma proteomics? by GenoMax 154k
> I performed a standard proteomics screening workflow What database did you use to search against? Perhaps you are using an old (not so c…
Answer: FACS quality control based on size and doublet detection in scRNA-seq by ATpoint 89k
No, it's unrelated. Doublets in 10x happen if two cells get enclosed into the same GEM droplet. This has nothing to do with how flow cytome…
Answer: How to handle TrEMBL proteins without gene annotation in plasma proteomics? by Elisabeth Gasteiger ★ 2.4k
Apparently you are working with human proteins? I would strongly recommend looking only at proteins that are part of the human reference pr…
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by colindaven 8.0k
Wow, thats too long. How much RAM does your machine have, it is likely swapping
Comment: How to handle TrEMBL proteins without gene annotation in plasma proteomics? by Elisabeth Gasteiger ★ 2.4k
Note that UniProtKB accession numbers do not have any meaning. While most ACs starting with A0A5* are indeed unreviewed (i.e. from TrEMBL),…
Comment: DESeq2 on metagenome KO counts by young_bioinformatician ▴ 240
Thank you but sorry, your answer sounds very AI-based...
Answer: How to handle TrEMBL proteins without gene annotation in plasma proteomics? by Aleksandra ▴ 180
For basic analysis, discard anything that isn't from Swiss-Prot. Your statistics and pathway analysis should only be based on reliable, ann…
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