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122,200 results • Page 614 of 2444
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2
votes
2
replies
1.4k
views
PCA results shows mixed population ?
imputation population stratification PCA
4.3 years ago by putty ▴ 40
0
votes
2
replies
1.2k
views
How to get orthologs between Two species in orthodb
Biomart Orthodb ortholog
4.3 years ago by hemantcnaik • 0
0
votes
2
replies
1.9k
views
VCF combination for common variants
dataframe VCF R
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 20
6
votes
4
replies
1.8k
views
Forum: What are the major advances in Bioinformatics since 2016
Bioinformatics
updated 2.7 years ago by 45k • written 4.3 years ago by ▴ 40
1
vote
0
replies
1.1k
views
Is it wrong to deconvolute bulk RNA seq data of a tissue using scRNAseq data of a different tissue?
deconvolution single-cell rna-seq
updated 3.4 years ago by 45k • written 4.3 years ago by ▴ 10
1
vote
2
replies
1.3k
views
I want to make a graph for conserved regions
COVID-19 MSA Conserved-regions
4.3 years ago by sa.youssef • 0
1
vote
0
replies
837
views
Forum: Potential applications of the AlfaFold ?
protein-folding
updated 4.3 years ago by ★ 90k • written 4.3 years ago by ▴ 220
0
votes
1
reply
1.5k
views
Comparison of two similar datasets with SCENIC
scrnaseq scRNA-Seq SCENIC GRN compare
updated 4.3 years ago by ★ 1.7k • written 4.3 years ago by • 0
2
votes
6
replies
2.9k
views
Understanding Gene Set Enrichment Analysis (GSEA) Tools in RNA-Seq
deseq2 pantherdb msigdb
updated 4.3 years ago by ▴ 320 • written 4.3 years ago by ▴ 20
0
votes
0
replies
658
views
Meta module definition
Wgcna eigengenes network
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 90
1
vote
1
reply
961
views
Plot a network based on correlation
correlation plot network RNAseq
updated 4.3 years ago by ★ 90k • written 4.3 years ago by ▴ 130
0
votes
4
replies
2.1k
views
FASTQ headers need additional info?
format FASTQ
4.3 years ago by Anand Rao ▴ 650
0
votes
1
reply
1.7k
views
Designing CNV analysis assay on Digital PCR
dPCR mitochondrial DNA CNV
updated 4.3 years ago by • 0 • written 8.3 years ago by • 0
0
votes
1
reply
1.1k
views
Pre-processing of BAMs before indel calling
indels DNA-seq bwa-mem bowtie2
updated 4.3 years ago by ★ 1.3k • written 4.3 years ago by ▴ 30
3
votes
1
reply
3.2k
views
What is the recommended contig length to filter?
metaspades
updated 4.3 years ago by ★ 30k • written 4.3 years ago by ▴ 260
0
votes
0
replies
856
views
PANTHER Gene List Analysis - Duplicate Genes (RNASeq Data)
DESeq2 pantherDB
4.3 years ago by Noah E. ▴ 20
0
votes
0
replies
952
views
CreateSomaticPanelOfNormals
GATK CreateSomaticPanelOfNormals PON
4.3 years ago by jhy ▴ 10
0
votes
0
replies
967
views
Modifying Genbank Contamination File for Bedtools
Genome-Assembly Linux
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 20
3
votes
6
replies
3.6k
views
how to filter out all the homozygous genotypes in a multi sample VCF file?
vcf
4.3 years ago by Nahid Bandi K • 0
9
votes
7
replies
8.8k
views
Aligning MiSeq targeted amplicons (ultra-deep sequencing)
Targeted-Sequencing MiSeq ultra-deep BWA Alignment
updated 3.9 years ago by 45k • written 11.2 years ago by ▴ 130
0
votes
0
replies
872
views
How do I make bwa-mem and bowtie2 less stringent?
DNA-seq bwa-mem bowtie2
4.3 years ago by gt ▴ 30
0
votes
2
replies
1.6k
views
How to extract reads for HLAscan
HLA genotyping NGS
4.3 years ago by from the mountains ▴ 250
2
votes
1
reply
1.6k
views
How were CCLE SNPs annotated?
annotation CCLE SNP
4.3 years ago by A. Domingues ★ 2.7k
0
votes
2
replies
1.3k
views
inquiry related to rsid
TWAS vcf rsid predixcan
updated 2.7 years ago by 45k • written 4.3 years ago by ▴ 150
1
vote
4
replies
5.4k
views
Sequencing depth with 10x Genomics
10x cell RNA-seq single
updated 4.3 years ago by ★ 19k • written 4.3 years ago by ▴ 10
1
vote
0
replies
837
views
Tool: BIRCH Bioinformatics System v3.80
alignment RNA-seq genome assembly sequence phylogeny
4.3 years ago by brian.fristensky ▴ 460
1
vote
4
replies
1.8k
views
guilt by association
pathways analyses R
4.3 years ago by pinheirofabiano ▴ 130
1
vote
17
replies
5.2k
views
SNP filtering
vcf SNP
updated 2.7 years ago by 45k • written 4.3 years ago by ▴ 150
0
votes
0
replies
815
views
RNA-seq differential expression analysis at specific defined intervals (downstream 1kb adjacent region to repetitive elements)
RNA-seq
4.3 years ago by jennxyzhang • 0
0
votes
0
replies
798
views
Multiome analysis: MAESTRO or Cell Ranger ACR
intergration multiome scRNA-seq scATAC-seq data
4.3 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 2.5 years ago by 45k • written 4.4 years ago by ▴ 10
0
votes
4
replies
1.5k
views
Microarray Data in R, Annotation of Transcript clusters
RStudio affy microarray
updated 4.3 years ago by ★ 90k • written 4.4 years ago by • 0
1
vote
3
replies
2.7k
views
How to filter VCF by the variant allele depth of a specific sample
bcftools VCF
4.4 years ago by john_campbell1 • 0
0
votes
11
replies
2.8k
views
error in R
RNASeq
updated 4.3 years ago by 45k • written 4.4 years ago by ▴ 10
1
vote
1
reply
2.6k
views
PLINK Error: Too many distinct nonstandard chromosome/contig names.
PLINK
updated 4.4 years ago by 11k • written 4.4 years ago by ▴ 140
0
votes
0
replies
965
views
metascape or STRING
Metascape STRING
4.3 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 4.4 years ago by 154k • written 4.4 years ago by • 0
2
votes
5
replies
6.3k
views
How to get gseKEGG() to accept an input gene list?
clusterprofiler dose gene-enrichment-analysis R
updated 2.7 years ago by ▴ 30 • written 4.4 years ago by ▴ 20
16
votes
15
replies
16k
views
8 follow
BAM files compression
bam
updated 4.3 years ago by ▴ 240 • written 5.8 years ago by ▴ 750
0
votes
4
replies
1.8k
views
variant calling
mutect2
updated 4.3 years ago by ▴ 30 • written 4.4 years ago by • 0
0
votes
0
replies
687
views
rmaps fiel output
RBPs splicing rMATs rmaps
4.4 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 2.7 years ago by • 0 • written 4.4 years ago by ▴ 80
3
votes
4
replies
2.8k
views
clusterprofiler for comparing differentially expressed genes
clusterProfiler comparecluster
4.4 years ago by najibveto ▴ 130
0
votes
0
replies
777
views
pycoQC Report - Interval unit in output over time plot
QC pycoQC Nanopore
4.4 years ago by chrys ▴ 80
3
votes
2
replies
1.4k
views
How to retrieve total gene numbers per cluster
seurat R
updated 4.4 years ago by ★ 1.8k • written 4.4 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
4.4 years ago by smeeta • 0
2
votes
3
replies
3.1k
views
How to get GTF file of virus genome
genome gene assembly
updated 4.4 years ago by • 0 • written 5.4 years ago by ▴ 170
0
votes
0
replies
1.4k
views
Job: Computational Biologist
research biology nextgen mizzou computational
4.4 years ago by stinsons • 0
0
votes
1
reply
1.2k
views
Expression recursion level exceeded Error in Admixture using mac computer
admixture
4.4 years ago by alexis.diaz • 0
3
votes
2
replies
2.8k
views
Using 'expand' in snakemake target rule with constraints
snakemake glob_wildcards expand
4.4 years ago by cfos4698 ★ 1.2k
122,200 results • Page 614 of 2444
Recent Votes
strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
Answer: How can I easily remove overlapping transcripts, keeping only longest transcript
Answer: Log2 transformation is well used, but is there a good paper that can be used as
Answer: Flatten a GTF
Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
Can EdgeR of DeSeq be used for Single-cell RNA-seq?
Answer: Getting the overlap between two GTF files
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Recent Replies
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by samuel.a.odonnell ▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by Pierre Lindenbaum 166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by alexandrakortsi • 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by xinguok794 ▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types by shpak.max ▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets by GenoMax 154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
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