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2
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0
replies
60
views
Are these 10x samples too low quality for downstream analysis?
scrnaseq Seurat 10x cell single
6 hours ago by AHerik ▴ 40
0
votes
3
replies
287
views
Split chromosome into smaller fragments to save memory when build xg and gcsa index.
vg
updated 1 day ago by ▴ 740 • written 2 days ago by • 0
5
votes
2
replies
904
views
Universal Human Reference RNA Sample
RNA
updated 2 days ago by ▴ 80 • written 4.0 years ago by ▴ 100
1
vote
2
replies
230
views
Question about substitution of KEGG
annotation KEGG Functional gene
1 day ago by dxh0222 ▴ 10
0
votes
0
replies
153
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment
updated 1 day ago by 153k • written 2 days ago by ▴ 10
1
vote
1
reply
226
views
Deeptools PlotProfile
computematrix deeptool heatmap chip-seq bamcoverage
updated 2 days ago by 89k • written 2 days ago by • 0
845
votes
170
replies
196k
views
112 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 4 months ago by 3.6k • written 8.7 years ago by 103k
0
votes
0
replies
138
views
News: online course: Species occurrence data: download and cleaning with R
data-cleaning biodiversity species-ocurrence
2 days ago by Transmitting Science communication ▴ 70
2
votes
3
replies
332
views
Local Synteny Analysis with Uncharacterized Genes
synteny
updated 2 days ago by 22k • written 3 days ago by • 0
0
votes
2
replies
257
views
Help with metagenomics viral
sequencing genomic metagenomic virology virus
2 days ago by CECEL • 0
1
vote
3
replies
370
views
mummer4: how do I get the mapview executable?
mummer mapview
updated 3 days ago by 153k • written 3 days ago by ▴ 10
2
votes
3
replies
401
views
RTG (Real Time Genomics) docker image - Problem dealing with different VCFs
rtg vcf genomic cancer
updated 2 days ago by 23k • written 3 days ago by • 0
0
votes
0
replies
217
views
News: online course: R/Bioconductor for Mass Spectrometry and Proteomics
R Mass-Spectrometry Proteomics Bioconductor
3 days ago by Physalia-courses ★ 2.6k
2
votes
5
replies
512
views
How to obtain a refFlat file for the Rat
RefFlat_file Rat
updated 2 days ago by 153k • written 3 days ago by ▴ 70
0
votes
0
replies
261
views
News: Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment SingleCellWorkflow SingleCell SingleCellData
3 days ago by ludwig.geistlinger ▴ 20
1
vote
4
replies
625
views
Is a direct comparison of the number of up- and down-regulated genes meaningful?
RNA-seq
updated 3 days ago by 4.1k • written 4 days ago by ▴ 70
0
votes
0
replies
282
views
How to convert demultiplexed Fastq to PRGs if Adaptor and Barcode information is not provided?
Pipesnake Paleomix UCE Fastq
3 days ago by s.pal2 • 0
1
vote
0
replies
324
views
Custom Selection of GO Terms or Pathways in EnrichR Output
enrichR ggplot2 R Python RNA-Seq
3 days ago by mohammedtoufiq91 ▴ 270
2
votes
2
replies
2.3k
views
CUT&Tag signal normalization for generating bigWig files
CUT-TAG bigwig normalization
updated 2 days ago by 89k • written 5 days ago by ▴ 10
2
votes
2
replies
3.0k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
RNAseq replicates DESeq2 EdgeR
2 days ago by DareDevil ★ 4.4k
0
votes
2
replies
576
views
How to detect divergent domains in AlphaFold models (CDD/InterProscan not working, PyMOL alignment)
alphafold structural-analysis domain-prediction pymol
3 days ago by LLG • 0
0
votes
0
replies
331
views
Error, 'object too long to compress'
orthologs oma OMA
4 days ago by felix_langschied • 0
0
votes
0
replies
321
views
Two-sample Mendelian Randomization (MR) summary statistics
GWAS randomization mendelian
4 days ago by handecadir • 0
0
votes
1
reply
411
views
combat_met error: mu_hat_mat[, batches_ind[[jj]]] : subscript out of bounds
combat_met epigenetics
updated 2 days ago by 3.4k • written 5 days ago by ▴ 60
0
votes
3
replies
1.3k
views
dual-RNA seq combined reference alignment and quantification.
exon dualrnaseq quantification annotation CDS
updated 5 days ago by 153k • written 5 days ago by • 0
2
votes
2
replies
4.7k
views
Illumina and ONT reads comparison
assembly ont genome illumina hybrid-assembly
updated 5 days ago by 7.8k • written 5 days ago by • 0
1
vote
2
replies
6.1k
views
Motif analysis
jaspar Motif meme homer analysis
updated 5 days ago by 15k • written 5 days ago by • 0
2
votes
2
replies
5.9k
views
Dragon Motif Builder download link
Motif Dragon Builder Discovery
updated 4 days ago by 7.8k • written 5 days ago by • 0
0
votes
0
replies
4.2k
views
News: online course: Host and manage your R projects with Git & GitHub
Git GitHub R-projects
5 days ago by Transmitting Science communication ▴ 70
1
vote
4
replies
13k
views
Asking for unmapped genes in RNA sequencing via Galaxy
Galaxy
5 days ago by Atefeh • 0
0
votes
3
replies
8.5k
views
UMAP QC
scRNAseq Spatial transcriptomics UMAP
updated 5 days ago by ▴ 810 • written 5 days ago by • 0
2
votes
2
replies
11k
views
RNA-Seq - Strand-specific coverage for a paired library
Bowtie2 bam RNA-Seq alignment
updated 6 days ago by 15k • written 9 days ago by • 0
0
votes
4
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9.2k
views
RNA seq batch correction with technical replicates
batch-effect RNA-seq technical-replicates
3 days ago by Li • 0
1
vote
0
replies
7.2k
views
Forum: A plot twist to DropletQC (scRNAseq Nuclear Fraction-based empty droplet filter)
scRNAseq DropletQC Velocyto STARSolo
4 days ago by hsuknowledge ▴ 10
0
votes
2
replies
14k
views
Problem creating STRUCTURE inputs with PLINK
vcf population plink structure genetics
updated 6 days ago by • 0 • written 13 days ago by ▴ 210
1
vote
1
reply
11k
views
Forum: Quick career guidance request - B.Tech final year
Biology Bioinformatics Masters Computational
updated 6 days ago by ★ 19k • written 6 days ago by • 0
0
votes
2
replies
10k
views
Confusion regarding genome coordinates in Genbank of TP53
isoform tp53 genbank
4 days ago by strontium • 0
0
votes
0
replies
7.9k
views
News: online course: Latent Class, Markov and Hidden Markov Models with Applications in R
MarkovModels HiddenMarkavModels LatentClass R
6 days ago by Physalia-courses ★ 2.6k
0
votes
0
replies
7.9k
views
News: online course: Graphs with R: ggplot
data-visualization ggplot2 R
updated 6 days ago by 153k • written 6 days ago by ▴ 70
0
votes
0
replies
7.9k
views
News: Online course: Bioinformatic tools for transcriptomic data analyses
training transcriptomics RNA-seq course
updated 6 days ago by 153k • written 6 days ago by ▴ 70
0
votes
0
replies
8.0k
views
diff_robust is TRUE but passed_ss is FALSE?
DAA ancombc-2
7 days ago by sumin • 0
2
votes
2
replies
12k
views
Asking for source of the figure
Seeking
updated 7 days ago by ▴ 380 • written 7 days ago by • 0
0
votes
3
replies
10k
views
bamCoverage with DNAse-seq shift
bigwig dnase-seq visualization deeptools
updated 4 days ago by ▴ 700 • written 9 days ago by ▴ 160
6
votes
3
replies
13k
views
GSEA vs GO enrichment
go kegg gsea
updated 6 days ago by 89k • written 9 days ago by • 0
0
votes
0
replies
8.0k
views
Question about adaptive bootstrap and self-tuning MCMC as acceptable methodology for publication
Bootstrap Phylogenetics BEAST2 MEGA MCMC
updated 7 days ago by 153k • written 7 days ago by • 0
1
vote
7
replies
12k
views
Fungal Genome Assembly: In a messed up situation
Illumina Pacbio Nanopore assembly HiFi
updated 8 days ago by ★ 1.7k • written 10 days ago by ▴ 240
6
votes
4
replies
9.2k
views
Tool: Resource: A searchable library of 100,000+ scientific figures for visualization inspiration
visualization
updated 8 days ago by ★ 1.7k • written 9 days ago by ▴ 40
0
votes
0
replies
8.5k
views
Job: Assistant, Associate, or Full Project Scientist in Cell & Developmental Biology
Biology UCSD Cell
9 days ago by UCSDBioSci ▴ 30
1
vote
1
reply
8.9k
views
vg gbwt missing sample and haplotype metadata when created using minigraph-cactus with vg construct
construct gbwt vg minigraph-cactus
updated 9 days ago by ▴ 760 • written 9 days ago by ▴ 10
0
votes
1
reply
8.7k
views
trouble: getting gene names from chromosome location using intersect function in bedtools
intersect chromosome location geneIDs bedtools
updated 9 days ago by 153k • written 9 days ago by ▴ 10
121,804 results • Page 1 of 2437
Recent Votes
Universal Human Reference RNA Sample
Universal Human Reference RNA Sample
Are these 10x samples too low quality for downstream analysis?
Are these 10x samples too low quality for downstream analysis?
C: gmap error: Length XXXX of quality score differs from length XXX of nucleotides
Answer: Question about substitution of KEGG
Answer: Universal Human Reference RNA Sample
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Recent Replies
Answer: Split chromosome into smaller fragments to save memory when build xg and gcsa in by Jordan M Eizenga ▴ 740
I would say the answer is unfortunately no. It would be possible to make smaller individual XG indexes, but downstream subcommands in the V…
Comment: Question about substitution of KEGG by dxh0222 ▴ 10
Thanks for your recommendation! I think kofam_scan is suitable for me.
Comment: How to use CAFE from Orthofinder Results by san96 ▴ 190
Hi, are you referring to Orthogroups.GeneCount.tsv? Thank you.
Comment: Universal Human Reference RNA Sample by michael.j.apostolides ▴ 80
For example you can see it here, this is the first one in the table (SRR1215996): https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=ru…
Answer: Universal Human Reference RNA Sample by michael.j.apostolides ▴ 80
I believe here: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP025982 They are from the SEQC https://www-nature-com.proxy3.library.…
Answer: Question about substitution of KEGG by Mensur Dlakic ★ 29k
There is a tool that uses KEGG hidden Markov models and HMMer to scan individual proteins. It is not automated and may require some fiddlin…
Comment: Huge discrepancy between Pipseeker & DRAGEN for Pipseq data by 1769mkc ★ 1.3k
DRAGEN are you using dragen 4.4 release for your workflow?
Comment: RTG (Real Time Genomics) docker image - Problem dealing with different VCFs by Jeremy Leipzig 23k
Your strategy sounds ok but we would need to see your modified file and the exact command you ran to know what happened.
Comment: Huge discrepancy between Pipseeker & DRAGEN for Pipseq data by Arindam ▴ 10
I think for mapping to the reference genome
Comment: Local Synteny Analysis with Uncharacterized Genes by Joe 22k
+1 for `clinker`, came here to make the same suggestion
Comment: Help with metagenomics viral by CECEL • 0
Hi, thanks for answer! I'm using Kraken2, but the classified reads, when put on BLAST, didn't returned nothing, even in Viruses_db...
Comment: How to obtain a refFlat file for the Rat by GenoMax 153k
You can't mix and match genomes and annotation as we discussed in the prior thread. Are you using the genome from UCSC, if you are using th…
Comment: Huge discrepancy between Pipseeker & DRAGEN for Pipseq data by 1769mkc ★ 1.3k
"DRAGEN uses a newer method employing hashtables" you mean the reference builder?
Comment: Split chromosome into smaller fragments to save memory when build xg and gcsa in by 李经纬 • 0
I use `vg construct --region chrom:start-end` to restrict graph to a chromosome region.
Comment: Split chromosome into smaller fragments to save memory when build xg and gcsa in by 李经纬 • 0
I have tried to index various chromosome sets. - chrom1 only: `Memory usage: 2.53022 GB`. - chrom1-10: `Memory usage: 13.3299 GB`. - c…
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