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122,013 results • Page 296 of 2441
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4
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2.4k
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Filter out overlapping deletions from a VCF file.
vcf bcftools gvcf
updated 14 months ago by ▴ 210 • written 2.6 years ago by ▴ 210
1
vote
1
reply
563
views
error in duplicate identification
r RNA-seq
updated 2.6 years ago by 45k • written 2.6 years ago by • 0
0
votes
1
reply
738
views
How to import downloaded multiple TCGA data in R?
TCGAbiolinks R TCGA
updated 2.6 years ago by 89k • written 2.6 years ago by ▴ 110
2
votes
3
replies
1.5k
views
HaplotypeCaller GENOTYPE GIVEN ALLELES doesn't genotype given alleles
Gatk HaplotypeCaller VCF
updated 2.6 years ago by ★ 3.1k • written 2.6 years ago by ▴ 100
1
vote
6
replies
3.3k
views
Problem creating new conda environment
conda
updated 2.6 years ago by 45k • written 3.1 years ago by ▴ 350
2
votes
1
reply
1.1k
views
Why SpliceAI does not annotate variants in different transcripts as SpliceAI lookup does.
SpliceAI
2.6 years ago by Manuel ▴ 50
2
votes
3
replies
2.5k
views
Split a yaml file in to multiple files by keys
yq yml yaml
2.6 years ago by kani ▴ 10
0
votes
2
replies
1.2k
views
WARNING: reads from the same pair were found not adjacent to each
featureCounts
2.6 years ago by Kurk • 0
1
vote
1
reply
661
views
plink skipping categorical phenotype
plink
updated 2.6 years ago by 166k • written 2.6 years ago by • 0
1
vote
2
replies
1.5k
views
How to get gene list from GENCODE gtf file?
protein-coding GENCODE gene
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 60
0
votes
0
replies
700
views
Forum: NGSrich - hg38
Coverage NGSrich
2.6 years ago by RK • 0
0
votes
4
replies
2.6k
views
R:scheduled cores 1, 5 did not deliver results
mclapply R
updated 2.6 years ago by 45k • written 2.6 years ago by • 0
5
votes
2
replies
1.1k
views
I want to print only those lines which contain non repetitive amino acid sequences
Linux python awk sed
updated 2.6 years ago by 45k • written 2.6 years ago by • 0
2
votes
3
replies
2.9k
views
Job: R Shiny Developer
HTML Javascript Shiny R
updated 2.6 years ago by • 0 • written 5.3 years ago by ▴ 20
0
votes
0
replies
845
views
Tool: GraphBio: A shiny web app to easily perform popular visualization analysis for omics data
visualization heatmap volcano-plot
updated 2.6 years ago by 45k • written 2.6 years ago by • 0
0
votes
6
replies
1.8k
views
Recreating a SPAdes Assembly
fasta SPAdes Assembly BAM
updated 2.6 years ago by 45k • written 2.6 years ago by • 0
0
votes
0
replies
642
views
How do we know that the AMR genes/ MGEs in the contig sequence is on plasmid or Chromosome?
bacteria plasmid
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 170
1
vote
9
replies
2.3k
views
Split trio vcf file
bcftools VCF
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 140
0
votes
13
replies
3.0k
views
Use bcftools isec to find denovo mutations
mutations denovo
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 140
0
votes
1
reply
854
views
Recent GDC Data Updating Parameters
Cancer Hypermutation GDC TCGA
updated 2.6 years ago by 45k • written 2.7 years ago by • 0
0
votes
1
reply
1.4k
views
How can I avoid artifacts in gene set/pathway scoring by UCell and similar algorithms?
ssGSEA Seurat escape UCell
updated 2.6 years ago by 89k • written 2.6 years ago by • 0
1
vote
3
replies
2.3k
views
Finding genome build of bed, bim, fam
genome
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 10
1
vote
2
replies
1.1k
views
Is it possible to estimate the concentration or amount of cellular mRNA using RNA-Seq data?
RNA-seq DEG
updated 2.6 years ago by ▴ 20 • written 2.6 years ago by ▴ 110
0
votes
4
replies
2.1k
views
Calculation of gene expression 2^-ΔΔCt.
deltact qpcr pcr
2.6 years ago by eugene • 0
0
votes
1
reply
757
views
Genome build of POPRES?
POPRES
updated 2.6 years ago by ★ 3.0k • written 2.6 years ago by ▴ 10
0
votes
0
replies
619
views
Reference panel when doing local ancestry
plink gwas ancestry reference-panel
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 10
1
vote
3
replies
979
views
addGeneAnnotation.pl: not found
repeats
updated 2.6 years ago by ★ 30k • written 2.7 years ago by • 0
1
vote
4
replies
1.3k
views
Missing samples in the output vcf file created using GenotypeGVCFs in GATK
SNP GATK
2.6 years ago by kk.mahsa ▴ 150
0
votes
0
replies
828
views
News: Course - Analysis of PROKARYOTIC PANGENOMES
Genomics Pangenomes
updated 2.6 years ago by 45k • written 2.7 years ago by ★ 2.7k
0
votes
2
replies
1.4k
views
How to convert a .gbk or .faa to .pep as well a .gbk or .gff to .bed?
sequence-formats
updated 2.6 years ago by 45k • written 2.7 years ago by • 0
1
vote
1
reply
873
views
Annotating VCF and filtering via annotation
SNP VCF
updated 2.6 years ago by ★ 2.5k • written 2.7 years ago by ▴ 10
0
votes
0
replies
702
views
Seperate males and females samples from trio.vcf
vcf shell
2.7 years ago by anasjamshed ▴ 140
0
votes
0
replies
693
views
Annotate a series of genomic intervals using R as detailed as possible
bed bioconductor annotation R
2.7 years ago by octpus616 ▴ 120
0
votes
0
replies
874
views
LD plot generation in Haploview
SNPs Haploview plot LD Plink
2.7 years ago by Koustav Maiti • 0
0
votes
1
reply
887
views
How to decide the best threshold for filtering probes in limma
limma
updated 2.7 years ago by ★ 8.3k • written 2.7 years ago by ▴ 30
1
vote
4
replies
8.3k
views
Why wont my newick file from MEGA open in FigTree?
software error phylogenetic tree MEGA FigTree
updated 2.6 years ago by 22k • written 6.0 years ago by ▴ 10
1
vote
2
replies
1.4k
views
Build a 3d protein model to compare two TF alleles and test in-silico the protein-DNA binding efficiency
protein-modelling protein-DNA-binding
2.6 years ago by lessismore ★ 1.4k
0
votes
6
replies
1.7k
views
Correcting erroneous k-mers and removing rRNA sequences
QC
updated 2.6 years ago by 45k • written 2.7 years ago by • 0
1
vote
2
replies
945
views
Ballgown Differential Transcript Expression Output Table
RNA-Seq Ballgown Differential-Trasncript-Expression StringTie
2.7 years ago by galaxy • 0
2
votes
3
replies
980
views
Error when performing integration to correct for batch effects
integration
2.6 years ago by Chris ▴ 360
0
votes
1
reply
779
views
Parse BlastP gaps
blast xml
updated 2.6 years ago by ▴ 110 • written 2.7 years ago by • 0
3
votes
4
replies
1.6k
views
How to remove a gene before making a cellranger reference?
fasta gtf cellranger scRNAseq
updated 2.7 years ago by 89k • written 2.7 years ago by ▴ 160
1
vote
1
reply
1.0k
views
How to obtain independent introns bed file from gtf
s.pombe genomics gtftoools
updated 2.7 years ago by 45k • written 2.7 years ago by ▴ 10
4
votes
4
replies
3.3k
views
how to Automate the Retrieval of Variant-related Information from Pubmed, dbSNP, ClinVar, HGMD etc
next-gen genome SNP
updated 2.7 years ago by 45k • written 7.6 years ago by ▴ 330
0
votes
7
replies
2.0k
views
VQSR first step do not generating plots
WGS WES VQSR
2.6 years ago by Yoosef ▴ 60
2
votes
4
replies
1.6k
views
Genome data visualization
gff3 bed regions genome
2.1 years ago by polag01 ▴ 20
0
votes
6
replies
4.0k
views
Limma for batch effect correction
microarray batch-effect limma
updated 2.6 years ago by ★ 8.3k • written 2.7 years ago by • 0
0
votes
0
replies
937
views
deepTools bamCompare - RPGC normalisation not supported?
bamCompare deepTools RPGC normalisation
updated 2.7 years ago by 45k • written 2.7 years ago by ▴ 10
5
votes
3
replies
1.6k
views
News: March 13-16: Virtual Nextflow and nf-core training event in 5 languages
nf-core pipeline Nextflow
updated 2.6 years ago by ▴ 410 • written 2.7 years ago by 5.1k
0
votes
3
replies
1.6k
views
MGI Sequencing - Best Script for fixing FASTQ file headers coming from MGI Sequencer's
NGS
updated 2.7 years ago by 154k • written 2.7 years ago by • 0
122,013 results • Page 296 of 2441
Recent Votes
A: Bam And Indexed Bam Files
Answer: How to create a phylogenetic tree from 30 VCF files
Comment: Reading AD and other genotype information from the VCF file
Answer: 1 vs 1 DEG analysis in scrna seq data
Comment: installation of package ‘DESeq2’ had non-zero exit status
Answer: Recommendations for 200 SNP markers genotyping
Comment: Reasonable number of SNPs in a bacterial genome.
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Recent Replies
Answer: 1 vs 1 DEG analysis in scrna seq data by ATpoint 89k
The only option you have is to treat every single cell as a replicate. That has the obvious downside that any effect can be a donor-unique …
Answer: GUI commercial software for 10x single cell gene expression analysis by firestar ★ 1.7k
An open-source option: [kana](https://www.kanaverse.org/kana/).
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
Yes, we plan to make English the primary language of the Brave UI.
Comment: Reasonable number of SNPs in a bacterial genome. by michael.ante ★ 4.0k
If your bacterial species is a (human) pathogen, you might want to check outbreak analysis papers of that species. In general, you find t…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by lieven.sterck 16k
ok, missed that ... in any case that should not happen indeed. How did you determine that the files are not equal? I can indeed also see t…
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Ram 45k
Do you have a plan to make an English version of the UI?
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
This can visualize the parameters of the generated workflow, software, and scripts, and manage the docker process of the script, software, …
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by ATpoint 89k
Can you summarize in one sentence what the use case is? Is this a workflow manager?
Comment: Pseudogene - scarce info by ATpoint 89k
This reminds me strongly on my "masters" courses (doesn't deserve that name tbf). "Here is some poorly-described project with little to no …
Answer: scVI vs Harmony, which is better for cell type based clustering in brain tissue? by ATpoint 89k
There is no "better" is my experience. It always depends on the dataset. Try both and integrate your biological knowledge to decide which m…
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 190
I just wrote that I misunderstood your initial question.
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 190
What exactly did I not get?
Comment: Interpreting genomic features distribution for CUT&RUN peaks by rfran010 ★ 1.7k
If I understand correctly, you see increased signal at TSS sites compared to control (taller peaks in browser). However, 92% of the 450 siS…
Comment: combine VCF from diploid reference/haplotypes for the same sample by cmdcolin ★ 4.3k
this question is a little similar to your previous question (https://www.biostars.org/p/9614638/). just as added info, here is a tool calle…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by aj123 ▴ 130
As mentioned above, I just got the raw fastq files from the ftp site listed.
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