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121,906 results • Page 34 of 2439
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288
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Running NGSadmix with pre-calculated ancestral genotype freqs?
admixture ngsadmix lcwgs angsd
7 months ago by j.smout.1 • 0
5
votes
5
replies
936
views
Differential Expression and absolute expression
normal DEG tumour rna
7 months ago by jain72744 ▴ 10
0
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3
replies
685
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Mapping ~100-300bp Sequences to Metagenome-Assembled Genomes
assembly Metagenomic
updated 7 months ago by 153k • written 7 months ago by ▴ 10
0
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1
reply
390
views
Differetial analysis EdgeR
Differetial EdgeR analysis
updated 7 months ago by 89k • written 7 months ago by ▴ 20
2
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3
replies
472
views
Can I compare Gene Expression in T Cells from PBMCs vs. Tumor Tissue (for match samples)?
batch-effect-correction integration scRNAseq single-cell harmony
updated 7 months ago by 89k • written 7 months ago by ▴ 20
0
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2
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592
views
multiBamSummary
deepTools multiBamSummary reverse-strand
updated 7 months ago by 45k • written 7 months ago by • 0
1
vote
2
replies
698
views
How to convert CIGAR string to VCF?
CIGAR VCF alignment variant-calling
updated 7 months ago by 45k • written 7 months ago by 3.2k
5
votes
6
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937
views
Extract FUngal mRNA from RNAseq Data
rnaseq rna fungus humant2t transcriptomics
6 months ago by SomeOne ▴ 240
0
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1
reply
574
views
PyMOL truncates part of structure when exporting as .pdb
pymol
updated 7 months ago by ★ 30k • written 7 months ago by • 0
0
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0
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1.5k
views
Job: Research Technician (Bioinformatics Analyst) - Computational Biology Core, Institute for Systems Genomics, UConn
Bioinformatics-Analyst Research-Technician
7 months ago by spu24005 • 0
0
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1
reply
558
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CLI Downloading from Human Microbiome Project Given Login + contact failure
Microbiome HMP
updated 7 months ago by 3.4k • written 7 months ago by ▴ 70
1
vote
2
replies
672
views
How to predict targets of miRNAs with indels in the seed region?
seed indels targets miRNA
updated 7 months ago by 89k • written 7 months ago by • 0
0
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2
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1.8k
views
News: FINAL CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (March 17-19, 2025 in Berlin, Germany)
transcriptomics scRNAseq singleCell
7 months ago by ecSeq Bioinformatics ▴ 20
3
votes
6
replies
4.1k
views
How To Retrieve The Rna Type From A Pdb File?
rna pdb
updated 7 months ago by ▴ 20 • written 13.5 years ago by ▴ 60
2
votes
1
reply
713
views
How to Analyze 10x Genomics Data with Full-Length R1 and R2 (100bp Each)?
10x-Genomics UMI single-cell RNA-Seq CellRanger
updated 7 months ago by 153k • written 7 months ago by ▴ 30
0
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0
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303
views
Mapping OMIM IDs (for diseases) to MeSH IDs
phenotype ontology DISEASE MESH OMIM
7 months ago by singhankit973 ▴ 20
1
vote
3
replies
1.6k
views
Gini Coefficient and Lorenz curve to measure uniformity of coverage
gini lorenz curve coverage uniformity
updated 7 months ago by ★ 1.2k • written 5.6 years ago by ▴ 70
2
votes
6
replies
1.2k
views
DESeq2 for multiple groups
usegalaxy Limma voom Deseq2
7 months ago by banaalkhayrat123 • 0
1
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2
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763
views
Bowtie index size / richness matters ?
bowtie
7 months ago by maschi88 • 0
0
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0
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478
views
juicer_tools for analyzing Hi-C data
juicer_tools
7 months ago by Bioinformatics_16 • 0
0
votes
1
reply
501
views
Limma Voom
Differential analysis
updated 7 months ago by 89k • written 7 months ago by ▴ 20
0
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0
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398
views
Blog: Novogene Single-cell and Spatial Multi-omics Case Study: Application in Bone Regeneration
Multi-omics Single-cell
7 months ago by Novogene ▴ 510
0
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1
reply
441
views
SNP density visualization with circos in galaxy
visualization CIRCOS
updated 7 months ago by 166k • written 7 months ago by • 0
0
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2
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660
views
Unusual File Count in 10x scMultiome Data for Cell Ranger ARC Processing
scMultiome 10x fastq human-cell-atlas cellranger-arc
7 months ago by Wu-Sheng Zhang • 0
0
votes
2
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653
views
Merge Seurat objects
seurat merge single-cell
updated 7 months ago by 45k • written 7 months ago by ▴ 110
0
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0
replies
490
views
News: Online Course: Network Analysis in R (May 5-8)
R NetworkAnalyis Tidyverse
7 months ago by Physalia-courses ★ 2.6k
0
votes
1
reply
608
views
News: Short Survey on Genomic Data Management & Analysis Workflows
Analysis Genomics
updated 7 months ago by 23k • written 7 months ago by • 0
0
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1
reply
565
views
Motif enrichment across super-enhancer regions
motif HOMER enrichment
updated 7 months ago by ★ 1.6k • written 7 months ago by • 0
0
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0
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417
views
JASPAR Database
JASPAR HOMER
7 months ago by sk_24 • 0
2
votes
4
replies
926
views
How to perform Linkage Disequilibrium (LD) analysis in INDELS
SNPs PLINK linkage disequilibrium haploview
updated 3 months ago by • 0 • written 7 months ago by ▴ 40
0
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0
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360
views
Spatt2.1 a mirMap dependency, anyone know where I can get it?
miRmap dependency tarball
7 months ago by RNAseqer ▴ 280
0
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0
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460
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DeChat Nanopore read correction with Medaka correction?
ont medaka wgs dechat nanopore
7 months ago by Mark ▴ 60
0
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1
reply
679
views
Why are phenotype values missing in PLINK analysis despite no NA values in the input?
PLINK PRS PHS PGS SNPanalysis
updated 7 months ago by 11k • written 7 months ago by • 0
2
votes
2
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816
views
Should I not have any adapters after trimming?
RNA-seq
updated 7 months ago by 15k • written 7 months ago by ▴ 160
2
votes
6
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1.4k
views
Incorrect gene naming (SYMBOL)
Gene-annotation
updated 7 months ago by 45k • written 7 months ago by ▴ 70
1
vote
1
reply
2.1k
views
Problem after subset of single cell integrated dataset in seurat using sctransform
seurat integration scRNAseq sctransform subset
7 months ago by NGS_enthusiast • 0
3
votes
6
replies
1.2k
views
Why do people say it doesn't matter whether you run unassembled or assembled reads through Kraken?
assembly unassembled-reads Kraken
6 months ago by trkfs ▴ 10
3
votes
5
replies
2.4k
views
Best way to provide sequences to Local Colabfold to not overload their mmseq2 server
Local ColabFold
updated 7 months ago by ★ 3.1k • written 7 months ago by ▴ 30
5
votes
9
replies
3.7k
views
Preventing Conda/Mamba from accessing Anaconda repos when institution blocks them
conda mamba repos miniforge channels
updated 7 months ago by ▴ 880 • written 7 months ago by ▴ 380
0
votes
1
reply
562
views
GO Analysis Combine or Separate DEGs
clusterProfiler GO
updated 7 months ago by ★ 2.0k • written 7 months ago by • 0
1
vote
1
reply
661
views
scType on Xenium Spatial Transcriptomics
Spatial Xenium scType
updated 7 months ago by ▴ 20 • written 7 months ago by ▴ 10
0
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0
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392
views
How to extract the components of a cluster after pheatmap
Heatmap Export Cluster
7 months ago by Luiza • 0
0
votes
1
reply
1.1k
views
Interpretation of MSMC2/PSMC/betaPSMC/ngsPSMC
Demography PSMC MSMC
updated 7 months ago by • 0 • written 11 months ago by • 0
0
votes
3
replies
904
views
Metagenomic binnig step
binnig tools Metagenomics
updated 7 months ago by ★ 30k • written 7 months ago by ▴ 30
0
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1
reply
582
views
Tool to phase genotyped large SV from short-read data?
sv structural variant short-reads haplotype phasing
updated 7 months ago by 166k • written 7 months ago by • 0
0
votes
0
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348
views
Normalisation for sample splice junction profiles
splicing normalisation RNAseq
7 months ago by coolmattmonkey • 0
0
votes
0
replies
402
views
Calculate base pair probability differences between Wild type and mutant sequences
probabilities rnaplfold rnafold basepair
7 months ago by RK • 0
0
votes
1
reply
647
views
What is indicated by the red dotted lines in the `tiny_10x_pbmc.pdf` out put from `cellbender remove-background`
remove-background cellbender
updated 7 months ago by 6.5k • written 7 months ago by ▴ 30
2
votes
4
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1000
views
Parameters for annotation with maker
Maker masking plant annotation
3 months ago by san96 ▴ 190
5
votes
3
replies
768
views
Extracting Sequences from a FASTA File Using Exon Coordinates from a GTF File
gtf fasta
updated 7 months ago by 7.9k • written 7 months ago by ▴ 20
121,906 results • Page 34 of 2439
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Answer: Tried building a compact sequence format with 4-bit storage
Tried building a compact sequence format with 4-bit storage
Shift in RNA 3' position, Term-Seq vs RNASeq
Comment: STARlong for pacbio Isoseq reads
Comment: Automatically annotating a feature using a genbank file
Answer: Is this PCA plot correct??
Answer: Is this PCA plot correct??
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Comment: Is total miRNA in EV constant? Implications for library size normalization. by Gordon Smyth ★ 8.3k
RNA-seq is very good at relative analyes. It would be straightforward to determine which miRNAs are relatively more abundant, compared to o…
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
Woah!!! Thank you very much, Matthias. I honestly didn't even know some of those existed and I will definitely go through them and try to u…
Answer: Tried building a compact sequence format with 4-bit storage by Matthias Zepper 5.1k
Hello Pranava, Thanks for sharing your repository. Devising a new file format is an interesting undertaking and certainly a task with many…
Answer: Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio) by GenoMax 153k
`LOC` gene ID's are often assigned to uncharacterized genes and you may not get useful information from databases for them, thus they will …
Comment: Whole Genome Sequencing IG regions by GenoMax 153k
> are the calls I am seeing reliable or should I take them with something of a pinch of salt? Not sure what calls you are referring to but…
Comment: RNA-SEQ where only a subset of genes is of interest by piffelpaff • 0
Sorry to revive this ancient thread but I'm currently discussing the same question with some people in my lab and would love to somebody po…
Answer: STARlong for pacbio Isoseq reads by YuZJ • 0
Hello, you may try deSALT (DOI: 10.1186/s13059-019-1895-9, GitHub: ydLiu-HIT/deSALT) or uLTRA (DOI: 10.1093/bioinformatics/btab540, GitHub:…
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq by acvill ▴ 350
Without knowing the details of the Term-seq method, could the 38 nt shift be accounted for by the difference in the position of the ribosom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
Thanks, I'll give it a try.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
You could give `mapPacBio.sh` from BBMap suite a try while you wait for other answers. That works for reads up to 6 kb. BBMap has a new hom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
The average is 1.8kb. I was planning to post it on GitHub, but it seems like the repository has been unattended for the last months, so I d…
Comment: Getting just fastqc.zip file? by GenoMax 153k
Yes, You can either use it on command line or use the graphical user interface.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
What is the average length of your reads? That error sounds like a bug, so you may want to post that on `STAR` repo as an issue. I assume …
Comment: Getting just fastqc.zip file? by pourhangleila95 • 0
I want to perform fastQC on my data.Do you use fastQC software for doing it?
Comment: Whole Genome Sequencing IG regions by 719 • 0
Sorry for the poor wording of the original post, also should say I really appreciate people taking a moment to look at my post. My main con…
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