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0
votes
1
reply
536
views
How to draw a Manhattan diagram based on the gene names?
gwas manhattan-plot r
updated 12 months ago by 45k • written 12 months ago by • 0
0
votes
1
reply
674
views
Trying to extract ONLY protein sequences with Augustus
Augustus gff sequences protein
updated 12 months ago by ★ 3.1k • written 12 months ago by • 0
3
votes
3
replies
1.4k
views
Identify SNPs with Fst estimates > 0.9 and annotate them
snpeff fst SNP
updated 12 months ago by 166k • written 2.4 years ago by ▴ 140
0
votes
0
replies
328
views
Error with KissDE exploreResults()
kissplice kissDE
12 months ago by david.b.rombaut ▴ 10
0
votes
2
replies
657
views
Different result in same species in jellyfish(genome size estimation)
jellyfish genome size
12 months ago by ylkim9 • 0
0
votes
2
replies
815
views
ESTIMATE -tidyestimate package- tumour purity
ESTIMATE Tumour-purity
12 months ago by Nona ▴ 90
4
votes
13
replies
3.5k
views
Can't reproduce harmony results in Seurat
Seurat scRNA-seq harmony
12 months ago by fifty_fifty ▴ 90
3
votes
3
replies
1.1k
views
Tool: Drawing circular and linear mitochondrial genome diagrams
mitochondria graphics mitogenomics
updated 12 months ago by 20k • written 12 months ago by ▴ 50
4
votes
2
replies
863
views
Weird looking volcano plot
Proteomics Volcano-plot Plasma
updated 12 months ago by ▴ 30 • written 12 months ago by ▴ 10
1
vote
4
replies
1.0k
views
Weird outcomes from employing NMF on scRNA-seq data
NMF scRNA-seq
11 months ago by tujuchuanli ▴ 130
2
votes
3
replies
1.1k
views
Statistics of methylation experiments
methylation
updated 12 months ago by ▴ 820 • written 12 months ago by ▴ 60
0
votes
0
replies
469
views
News: Course: Metabarcoding in Microbial Ecology
R Qiime2 Metabarcoding Microbial-Ecology
12 months ago by Physalia-courses ★ 2.6k
3
votes
6
replies
2.5k
views
Representable, non-homologous, non-redundant protein database
non-homologous representable non-redundant database proteins
updated 12 months ago by • 0 • written 3.8 years ago by ▴ 80
0
votes
0
replies
387
views
GWASQC
gwas
12 months ago by karthick ▴ 10
0
votes
1
reply
831
views
ADNI DATASET
ADNI
updated 12 months ago by 7.9k • written 2.0 years ago by ▴ 10
4
votes
2
replies
992
views
gatk-funcotator data source
gatk datasource germline funcotator
12 months ago by ashaneev07 ▴ 50
2
votes
2
replies
856
views
how to order paired-end reads to use in kaiju?
taxonomy paired-end-reads Kaiju
updated 12 months ago by 45k • written 12 months ago by • 0
1
vote
1
reply
453
views
Any tutorial on Braker3
tutorial Braker3
updated 12 months ago by ★ 30k • written 12 months ago by • 0
0
votes
2
replies
1.1k
views
What type of graph or visualization would be most appropriate to represent this data for effective comparison of insertion times across sequences?
pacBio NUMTs mtDNA Genomics
updated 12 months ago by 45k • written 12 months ago by ▴ 40
0
votes
2
replies
1.4k
views
Converting genome build from hg38 to hg19 using liftOver via bigsnpr - error fetching file
snp bigsnpr liftover r
updated 12 months ago by • 0 • written 13 months ago by ▴ 200
3
votes
6
replies
2.1k
views
Error Code 3 with fastq-dump
fastq-dump
updated 12 months ago by 153k • written 12 months ago by • 0
1
vote
0
replies
397
views
Meta-analysis with 2 GEO transcriptomic datasets possible?
Meta-analysis GEO
12 months ago by Dr. ▴ 20
13
votes
5
replies
8.5k
views
6 follow
Programs for drawing a circular mitochondrial map, Circos or others?
Circos circular-map
updated 12 months ago by 45k • written 9.4 years ago by ▴ 110
0
votes
0
replies
438
views
Understanding how to analyse VEP files and understand the impact of mutations on biological pathways
REACTOMEPA SNV VEP GO
12 months ago by namg • 0
1
vote
0
replies
466
views
Tool: Welome to try Circle-Map++ for detecting eccDNA
eccDNA ecDNA DNA Circle-Map Circular
12 months ago by xiaoguang ▴ 160
0
votes
2
replies
772
views
Aedes vexans RNA-seq de novo assembly
de-novo RNA-seq Aedes
updated 12 months ago by 20k • written 12 months ago by ▴ 20
3
votes
2
replies
928
views
In Plink2, when converting a VCF file to bed format - how to retain original chromosome names?
plink2 vcf
12 months ago by rijan_dhakal2055 ▴ 10
0
votes
0
replies
396
views
1000 genomes's reference panel
vcf reference genetics
12 months ago by Hasan_Daaboul • 0
1
vote
0
replies
567
views
How to identify temporal differential gene expression patterns among cell types in scRNA-seq
gene-expression dynamic scRNA-seq DEGs
updated 12 months ago by 45k • written 12 months ago by ★ 1.3k
0
votes
0
replies
556
views
News: Introduction to Nextflow course
Nextflow Pipeline Workflow-Manager Reproducibility
updated 12 months ago by 45k • written 12 months ago by ★ 2.6k
1
vote
1
reply
722
views
Quality check pipeline for PCR cDNA ONT sequencing output.
ONT-PCR-cDNA Long-Reads RNA-seq Transcriptome
updated 12 months ago by 45k • written 12 months ago by ▴ 10
5
votes
1
reply
857
views
p value of significance for overlapping peaks
MACS2 Chip-seq
updated 12 months ago by 22k • written 12 months ago by ▴ 40
5
votes
9
replies
3.8k
views
6 follow
Noob question. Samtools says my CRAM from Nebula is wonky, what can I do?
CRAM Nebula samtools
updated 12 months ago by ★ 1.3k • written 3.0 years ago by ▴ 80
3
votes
2
replies
2.0k
views
Job: Freelance Bioinformatician Required
picrust patric
updated 12 months ago by ★ 2.1k • written 13 months ago by • 0
0
votes
2
replies
886
views
CombatSeq introduces clustering in RNA-seq data (miRNA)
miRNA batch-correction rna-seq combat-seq
updated 12 months ago by 45k • written 12 months ago by • 0
6
votes
1
reply
838
views
identify sex in a FASTA RNA-Seq file
RNA-Seq
updated 12 months ago by ▴ 150 • written 12 months ago by ▴ 130
0
votes
1
reply
894
views
Help Needed: Importing and Analyzing GWAS Data from GWAS Catalog in R
R GWAS
updated 12 months ago by 45k • written 12 months ago by • 0
3
votes
5
replies
1.1k
views
Reporting novel species from environmental samples
bacteria 16S genomics
updated 12 months ago by 45k • written 12 months ago by ★ 2.9k
1
vote
2
replies
1.2k
views
Structural alignment of protein
structural-alignment protein
12 months ago by Sadik Muzemil ▴ 20
1
vote
2
replies
1.1k
views
Find RefSeq-Entries with Protein sequences by whether the organisms are considered to be part of (specific) microbiome
refseq microbiome
updated 12 months ago by ★ 30k • written 12 months ago by ▴ 10
0
votes
2
replies
148k
views
FastTree error: Non-unique name 'xxxxx' in the alignment
fasttree orthofinder phylogeny mafft
12 months ago by eedeaguiar • 0
0
votes
0
replies
461
views
Number of ESVs greater than OTUs'?
denoising otu asv
12 months ago by alenew.am ▴ 10
0
votes
1
reply
649
views
Hi-C analysis
HiC
updated 12 months ago by 153k • written 12 months ago by • 0
0
votes
0
replies
557
views
News: Beyond Beginner R: Advancing Your Coding Skills (Sept 16-19, 2024)
R Coding Reproducibility Programming
updated 12 months ago by 45k • written 12 months ago by ★ 2.6k
0
votes
4
replies
983
views
vcf file filtration w.r.t. missingness per snps and unmapped snps
missingness-per-snp unmaped-snps
12 months ago by analyst ▴ 70
0
votes
1
reply
720
views
find marker using scRNAseq data
scRNAseq biomarker
updated 10 months ago by ▴ 40 • written 12 months ago by ▴ 20
1
vote
1
reply
897
views
Gabor Wavelet Transform on DNA sequence in python
python signal-processing DNA
updated 12 months ago by 45k • written 12 months ago by ▴ 10
0
votes
0
replies
532
views
VCFTools Order of Flags Inquiry
vcf vcftools
updated 12 months ago by 9.8k • written 12 months ago by • 0
7
votes
8
replies
5.8k
views
9 follow
Forum: Dentist interested in bioinformatics
career
updated 12 months ago by ★ 2.9k • written 8.7 years ago by ▴ 10
0
votes
0
replies
557
views
News: gnomAD v4 is now available on OpenCRAVAT!
gnomad Genomics OpenCRAVAT gnomADv4
updated 12 months ago by 45k • written 12 months ago by ▴ 10
121,920 results • Page 72 of 2439
Recent Votes
Comment: cellranger mkref fail/error
A: read.table does not read in all rows!
A: read.table does not read in all rows!
A: Binning Over Genes And Calculating The Coverage [Bedops/Bedmap]
Answer: [vg giraffe] Unable to add read group to BAM file
Comment: [vg giraffe] Unable to add read group to BAM file
Answer: [vg giraffe] Unable to add read group to BAM file
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Recent Replies
Comment: cellranger mkref fail/error by ATpoint 89k
I think OCM = https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-3p-what-is-cellplex#on-chip Seconding to…
Comment: miRNA low mapping ratings by Ant ▴ 50
The first one it's the results from Cutadapter and the second block from miRDeep2.
Comment: miRNA low mapping ratings by Ant ▴ 50
Thanks for the reply, when running: cutadapt -a AACTGTAGGCACCATCAAT -M 30 -o example_trimmed.fastq.gz data/xxx.fastq.gz, the sequence le…
Comment: Help with species tree with orthofinder, iqtree and branch labeling by GenoMax 153k
> I don’t have clear species labels in my headers, only sequence IDs. I have not used iqtree, so this is only a thought ... should it be y…
Comment: Help with species tree with orthofinder, iqtree and branch labeling by san96 ▴ 190
Thank you so much.
Comment: [vg giraffe] Unable to add read group to BAM file by saruman ▴ 10
Yes, it seems so. Thank you.
Comment: cellranger mkref fail/error by GenoMax 153k
> The thing is that I do not have a genome for these organisms. That is not what `cellranger mkref` is expecting. You could consider alt…
Comment: cellranger mkref fail/error by tatsispolychronis • 0
The thing is that I do not have a genome for these organisms. i made a transcriptome using TRinity and this is what I am feeding it. I do n…
Comment: Genome Assembly QC from BAM files by SomeOne ▴ 240
Hi, I am not sure if i can call them good assemblies. Although based on QUAST and BUSCO stats, everything looks too good but somehow i hav…
Comment: cellranger mkref fail/error by GenoMax 153k
You need to provide the genome reference for the `--fasta` option as noted in https://www.10xgenomics.com/support/software/cell-ranger/late…
Answer: Methods to analyse structural similarity: co-evolution vs convergence by Joe 22k
Without historical data (ancient DNA) there's no way to ever really know this for certain. The best we can do is make inferences based on t…
Answer: vcf multisample by Pierre Lindenbaum 166k
eg : https://ega-archive.org/datasets/EGAD50000001683 > Merged VCF file from sporadic Meniere disease cohort (found using https://dat…
Comment: Genome Assembly QC from BAM files by GenoMax 153k
Since this saga has been on going for a long time, it will be helpful to add a comment as to how you finally got to this point of what seem…
Comment: Methods to analyse structural similarity: co-evolution vs convergence by dthorbur ★ 3.1k
A few comments. 1. Coevolution of a trait between 2 organisms can end up with a convergent structure with another organism. It's not e…
Comment: Genome Assembly QC from BAM files by SomeOne ▴ 240
Thank you. Based on the description these two look really what i wanted to see.
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