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122,229 results • Page 3 of 2445
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2
votes
2
replies
556
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Critique or Feedback of filtering strategy for LIANA+ results using spatially informed bivariate metrics
LIANA spatial-transcriptomics visiumHD
13 days ago by danielpintard ▴ 10
2
votes
20
replies
7.4k
views
8 follow
PacBio raw data trimming and cleaning
pacbio trimming cleaning qc
updated 13 days ago by 16k • written 6.8 years ago by ▴ 110
0
votes
0
replies
190
views
News: Online Course - A Practical Introduction to NGS Data Analysis (December 3-5, 2025) - 32% Off
VariantCalling Illumina Workshop DNA-Seq RNA-Seq
14 days ago by ecSeq Bioinformatics ▴ 20
0
votes
10
replies
820
views
Count unique fragments from a given BAM file
dna bam
updated 14 days ago by 154k • written 14 days ago by ▴ 520
0
votes
2
replies
2.6k
views
Merlin ped file issue
linkage merlin
updated 8.1 years ago by • 0 • written 8.7 years ago by ▴ 10
1
vote
2
replies
9.0k
views
GO Terms significance Scoring
go semantic annotation
updated 14 days ago by ▴ 480 • written 3 months ago by • 0
6
votes
2
replies
550
views
Ribo-seq Trimming Issue: Massive Read Loss in Paired-end Mode
trimming paired-end riboseq
updated 14 days ago by ▴ 150 • written 21 days ago by ▴ 10
1
vote
1
reply
266
views
Running snpEff with hg19 reference genome (config file question)
snpEff hg19
updated 14 days ago by 166k • written 14 days ago by ▴ 70
1
vote
3
replies
1.6k
views
Error when opening CEL files in python
python
written 4.2 years ago by • 0
0
votes
2
replies
726
views
NAT Vs T samples DA analysis
abundance differential microbiome
updated 15 days ago by ★ 90k • written 22 days ago by • 0
0
votes
1
reply
1.4k
views
problem with reading cel files from [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [HuGene20stv1_Hs_ENTREZG_17.0.0]
normalization microarray
updated 15 days ago by ★ 90k • written 12 months ago by • 0
0
votes
0
replies
538
views
How to select background metabolite sets for differential metabolite enrichment analysis?
enrichment ORA
updated 15 days ago by ★ 90k • written 7 weeks ago by • 0
0
votes
1
reply
733
views
How much coverage is needed for high-quality phylogenetic and admixture analyses using short-read WGS in plants?
coverage
updated 15 days ago by ★ 90k • written 8 weeks ago by • 0
0
votes
2
replies
988
views
Does the weights file stay the same for a different model organism
machine-learning
updated 15 days ago by ★ 90k • written 6 weeks ago by • 0
1
vote
4
replies
5.6k
views
SNP calling with bacterial assembled genome
variant-calling SNP bacteria
updated 15 days ago by ★ 90k • written 9 weeks ago by • 0
0
votes
1
reply
590
views
Best way to map biological pathways to cancer hallmarks using PLMs (without building models)?
PLM mapping LLM extraction Relation
updated 15 days ago by ★ 90k • written 7 weeks ago by • 0
0
votes
1
reply
573
views
Small Molecule Databases and clustering
polyethylene MolecularDatabase Molecule PET trephthalate
updated 15 days ago by ★ 90k • written 12 months ago by ▴ 10
2
votes
2
replies
874
views
Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
data transcriptomic
updated 15 days ago by ★ 90k • written 12 months ago by • 0
0
votes
2
replies
990
views
Clustal omega on M1 Mac
alignment clustal-omega MacOS
updated 15 days ago by ★ 90k • written 12 months ago by • 0
1
vote
2
replies
830
views
Depth and genotype quality in vcf file
Vcf depth wes variants
updated 15 days ago by ★ 90k • written 12 months ago by ▴ 50
2
votes
5
replies
1.5k
views
Need help with fgsea
scRNAseq fgsea
updated 14 days ago by ★ 90k • written 12 months ago by ▴ 20
3
votes
3
replies
966
views
RNA-seq data compared to qRT-PCR
RNA-seq
updated 15 days ago by ★ 90k • written 12 months ago by ▴ 10
3
votes
3
replies
1.4k
views
biomart hangs
biomaRt
updated 15 days ago by ★ 90k • written 12 months ago by ▴ 60
4
votes
7
replies
1.4k
views
PCA interpretation
RNASeq PCA
updated 15 days ago by ★ 90k • written 12 months ago by ▴ 20
4
votes
28
replies
8.2k
views
8 follow
Did anyone manage to successfully run HLAScan and get results?
HLA-Typing NGS
updated 15 days ago by ★ 90k • written 7.5 years ago by ▴ 10
7
votes
30
replies
4.5k
views
What's the powerful biological methods for significant genes selection?
gene selection significant biological method R
updated 15 days ago by ★ 90k • written 7.0 years ago by ▴ 260
19
votes
44
replies
8.8k
views
Annotation of huge number of CNV files
CNV annotation TCGA
updated 15 days ago by ★ 90k • written 7.3 years ago by ▴ 530
4
votes
46
replies
10k
views
SAM file wrong? help with validatesamfile
EXOME
updated 15 days ago by ★ 90k • written 9.4 years ago by ▴ 110
16
votes
39
replies
20k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 15 days ago by ★ 90k • written 10.8 years ago by ▴ 920
41
votes
56
replies
16k
views
8 follow
hash function for DNA sequences
hash hashing DNA
updated 15 days ago by ★ 90k • written 9.7 years ago by ▴ 290
3
votes
4
replies
25k
views
Subsetting - Raw Counts from Seurat Object
seurat raw counts RNA-Seq
updated 15 days ago by ★ 90k • written 5.6 years ago by ▴ 500
5
votes
7
replies
37k
views
terminate called after throwing an instance of 'std::bad_alloc?
bedtools linux data
updated 15 days ago by ★ 90k • written 6.6 years ago by ▴ 350
4
votes
14
replies
41k
views
7 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 15 days ago by ★ 90k • written 7.8 years ago by ▴ 20
24
votes
23
replies
62k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink vcf fam gatk vcftools
updated 15 days ago by ★ 90k • written 7.6 years ago by ▴ 280
1
vote
1
reply
554
views
TOM matrix WGCNA
WGCNA
updated 15 days ago by ★ 90k • written 4 months ago by • 0
0
votes
1
reply
1.3k
views
Two-sample Mendelian Randomization (MR) summary statistics
GWAS randomization mendelian
updated 15 days ago by ★ 90k • written 3 months ago by • 0
0
votes
1
reply
1.3k
views
Error, 'object too long to compress'
orthologs oma OMA
updated 15 days ago by ★ 90k • written 3 months ago by • 0
2
votes
1
reply
287
views
KEGG Orthologs (KO) from 16S vs. Metabolites
picrust2 microbiome metabolome
updated 16 days ago by 3.9k • written 16 days ago by ▴ 10
1
vote
1
reply
498
views
Direct RNA-seq Nanopore
dRNA
updated 16 days ago by ★ 90k • written 21 days ago by • 0
0
votes
0
replies
341
views
Advice on choosing the best ChromHMM mode for CUT Tag data
CUT_TAG ChromHMM Histone
updated 16 days ago by ★ 90k • written 20 days ago by ▴ 10
2
votes
5
replies
6.5k
views
cellranger mkref fail/error
mkref multiple_species customtranscriptome cellranger transcriptome
updated 16 days ago by ★ 90k • written 10 weeks ago by • 0
1
vote
2
replies
515
views
Using soupX on single nucleus RNA seq data
rnaseq soupX singlenucleus snRNAseq
updated 16 days ago by ★ 90k • written 19 days ago by • 0
0
votes
2
replies
5.0k
views
TOPMed Imputation - More than 10000 allele switches
imputation topmed
updated 16 days ago by ★ 90k • written 3 months ago by • 0
0
votes
2
replies
4.9k
views
Question regarding batch effect in TCGA-HNSC
Cancer DESeq2 SVA TCGA
updated 16 days ago by ★ 90k • written 11 weeks ago by • 0
0
votes
0
replies
231
views
BLAST database error while using HiFiAdapterfilt to filter out adapter contaminants from PacBio raw reads
BLAST PacBio NCBI assembly genome
updated 16 days ago by ★ 90k • written 16 days ago by • 0
0
votes
0
replies
6.3k
views
rsid in full data table for GSA array but not in the final vcf file
array GSA
updated 16 days ago by ★ 90k • written 10 weeks ago by ★ 1.3k
0
votes
0
replies
5.9k
views
Radial plot help
Radial-Plots Bulls-eye
updated 16 days ago by ★ 90k • written 11 weeks ago by ▴ 10
5
votes
3
replies
533
views
Looking for Entry-Level Bioinformatics Project Ideas to Build My Portfolio
genomics next-generation-sequencing bioinformatics
16 days ago by Somudraneel ▴ 10
0
votes
1
reply
451
views
Is there a difference between signalValue and FoldEnrichment in peak files obtained by MACS2 peakcalling
chip-seq cutandrun
updated 16 days ago by ★ 1.7k • written 17 days ago by • 0
2
votes
2
replies
383
views
ATAC-SEQ FRAGMENT SIZE
Size Fragment Picard ATAC-seq
updated 17 days ago by ★ 90k • written 18 days ago by ▴ 10
122,229 results • Page 3 of 2445
Recent Votes
Answer: Chip-seq analysis Diffbind
Question about variant calling method using pangenome-graph
Comment: SyntaxError in file /snakefile, line 22: invalid decimal literal: None
Answer: Is this Rosalind inspired project actually useful?
Answer: Minimap2 segfaults when mapping Nanopore reads to a very large reference databas
Comment: How to normalize the intensity of bigwig files based on a group of house-keeping
Answer: Re-assembling old RNA-seq reads vs. using an existing transcriptome assembly
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Comment: Chip-seq analysis Diffbind by Irene ▴ 10
Thank you very much for always answering my doubts and questions. I truly value and appreciate it because it helps me understand the result…
Comment: Minimap2 segfaults when mapping Nanopore reads to a very large reference databas by firefox91 ▴ 10
Many thanks !
Answer: Re-assembling old RNA-seq reads vs. using an existing transcriptome assembly by GenoMax 154k
> I have access to both the raw reads and the previously assembled transcriptome submitted to TSA. and > I am trying to determine wheth…
Answer: Re-assembling old RNA-seq reads vs. using an existing transcriptome assembly by dthorbur ★ 3.2k
There are a few factors to consider: **The quality of the existing reference.** If there is a high quality chromosome level assembly,…
Comment: "sortmerna" quitting early--is this is a memory issue? by colindaven 8.1k
Pls add the output and your system (especially RAM), no one here can guess.
Answer: Power calculations for differentially methylated DNA samples from sequencing by colindaven 8.1k
There are software packages for power analysis such as https://academic.oup.com/bioinformaticsadvances/article/5/1/vbaf150/8173951.
Comment: Data integration single cell using Harmony by Arup Ghosh 3.5k
Run QC for each sample separately, then merge run SCTransform, PCA, then Harmony, UMAP, FindNeighbors and FindClusters.
Comment: Data integration single cell using Harmony by _deb • 0
Thank you for the quick answer. I still have a doubt. It would be better to pre-process each sample separately (*filtering, SCTransform…
Comment: Issue while running Kenddata. by rana.elromh • 0
I checked the memory before executing this command. I made a bash script on Ubuntu to run it on 15 folders. But, this problem happened in f…
Comment: Prokka output genes clusterization by function by Mensur Dlakic ★ 30k
Many proteins have multiple domains, and are correctly classified with multiple KO numbers. That's not a bug in `kofam_scan` but rather a r…
Comment: mapping sequences on specific region of bacteria genome by samuel.a.odonnell ▴ 650
If you want to visualise the mapping; take a look at using IGV. It just requires the genome you used to map the reads and the BAM output (n…
Comment: Prokka output genes clusterization by function by shevch2009 ▴ 20
Thanks, I had completely forgotten that METABOLIC works with protein sequences. That will work :) I was just trying to figure out how peop…
Answer: Prokka output genes clusterization by function by Mensur Dlakic ★ 30k
It is easy to install `kofam_scan` and get the output: https://github.com/takaram/kofam_scan What is the impediment to using METABOLI…
Answer: Manual corrections for allele mismatches by curious ▴ 900
take a look at thomas winkler's stuff: https://www.nature.com/articles/nprot.2014.071
Comment: Repeated Coordinate Errors (>171823) in NC_007605.1 (EBV) GTF Conversion (LMP2A/ by halo22 ▴ 300
Thanks for sharing this. I was able to get makeref to work.
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