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121,014 results • Page 7 of 2421
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0
replies
186
views
Cosmic database update issue in annovar
annovar cosmic genomics
updated 4 weeks ago by 45k • written 4 weeks ago by • 0
1
vote
1
reply
359
views
Transforming diploid GT on male X and Y chromosome to haploid
VCF genotype gVCF
4 weeks ago by Michaela ▴ 10
3
votes
3
replies
411
views
How do I figure out pangenome location of hg38 coordinates?
pangenome hg38 vg
updated 4 days ago by • 0 • written 4 weeks ago by ▴ 10
5
votes
7
replies
608
views
How I can curate all exon start-end positions for 50 genes (to create GTF file)?
gtf curation gene
updated 4 weeks ago by 150k • written 4 weeks ago by ▴ 10
0
votes
0
replies
179
views
generating manhattan plot through hail
plot manhattan hail visualizations gwas
4 weeks ago by nitya • 0
0
votes
0
replies
170
views
Hard Filtering Differences between WES and WGS
WES WGS Hard-Filtering
updated 4 weeks ago by 45k • written 4 weeks ago by • 0
0
votes
3
replies
358
views
Am I accounting for replicates correctly in pseudobulk analysis?
deseq2 single-cell pseudobulk
updated 4 weeks ago by 87k • written 4 weeks ago by ▴ 370
2
votes
4
replies
494
views
Is there too little variation to detect meaningful gene changes?
DESEQ
updated 4 weeks ago by 102k • written 5 weeks ago by ▴ 50
3
votes
5
replies
486
views
nanopore SNV callers returns empty VCF
snv_caller nanopore
updated 26 days ago by 102k • written 4 weeks ago by ▴ 10
15
votes
3
replies
1.3k
views
Tutorial: Avoiding the Pitfalls of the Anaconda License: A Practical Guide
conda Anaconda license
4 weeks ago by Juke34 9.2k
0
votes
2
replies
288
views
How many cells are needed in subcluster to draw conclusions?
immunology T-cells scRNA-seq
4 weeks ago by S • 0
0
votes
2
replies
283
views
Question about assigning gene names, tximport and DESeq2
tximport deseq2
9 days ago by bioinfo ▴ 150
3
votes
3
replies
403
views
RNASeq: Confused about adapters with barcodes and seq company's filtering
atria rnaseq adapter-trimming
updated 4 weeks ago by 150k • written 4 weeks ago by • 0
1
vote
2
replies
325
views
VEP won't show symbols for all variants; SnpEff will, but won't for others
vep snpeff
updated 4 weeks ago by 23k • written 4 weeks ago by ▴ 20
0
votes
2
replies
264
views
How to plot LMER estimate values in heatmap ?
cell scRNAseq TF lmer transcription
4 weeks ago by carolofharvest ▴ 50
1
vote
2
replies
1.3k
views
News: Final Call - Next-Generation Sequencing Data Analysis: A Practical Introduction (April 2-4 in Munich) - Only 2 seats left
Workshop RNAseq Variant-Calling Illumina DNAseq
4 weeks ago by ecSeq Bioinformatics ▴ 20
0
votes
1
reply
235
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
tehnical-replicates DESeq2 RNA-Seq
updated 4 weeks ago by 45k • written 4 weeks ago by • 0
0
votes
3
replies
366
views
Can anyone help me download the dbSNP data for Bos taurus ARS-UCD1.3?
GWAS genetics WGS
updated 4 weeks ago by 45k • written 4 weeks ago by • 0
0
votes
1
reply
248
views
Co-expression analysis of miRNAs and target mRNAs
miRNA targets co-expression miRNA-mRNA
updated 4 weeks ago by 21k • written 4 weeks ago by ▴ 40
0
votes
0
replies
177
views
Beagle Imputation
Beagle Imputation
4 weeks ago by mahlet.teka • 0
0
votes
0
replies
284
views
Issue with bam-readcount and fpfilter.pl: Saying "failed to get readcounts for variant allele"
bam-readount somaticsniper
updated 4 weeks ago by 166k • written 4 weeks ago by • 0
2
votes
2
replies
315
views
miRNA-seq: QC reports and workflow
miRNA-seq ION-Torrent RNA-seq FASTQC
4 weeks ago by omicon ▴ 40
1
vote
0
replies
158
views
How to Run Large-Scale Foldseek Comparisons (Human vs. C. elegans)
c.elegans Foldseek Genes Orthologs Homologs
4 weeks ago by bioinformatics_rk ▴ 10
0
votes
1
reply
271
views
Recommendations for Reference-guided de novo assembly assembly approaches or pipelines?
ont assembly wgs nanopore genomics
updated 4 weeks ago by ★ 1.5k • written 5 weeks ago by ▴ 30
0
votes
1
reply
243
views
Per Base Sequence Content FastQC
RNA-seq quality-control
updated 4 weeks ago by ★ 1.5k • written 5 weeks ago by ▴ 20
3
votes
2
replies
379
views
Seeking Advice on Handling Multiple Datasets for Differential Analysis in Transcriptomics
Data-Integration Differential-Analysis Transcriptomics Data-Normalization
4 weeks ago by Riley J • 0
2
votes
3
replies
341
views
Population genetics with mutect2 data
haplotypecaller mutect2
updated 4 weeks ago by 4.7k • written 5 weeks ago by • 0
1
vote
2
replies
277
views
ggplot of two data set with different colors
geom_line scale_colour_manual ggplot2
updated 5 weeks ago by • 0 • written 5 weeks ago by ▴ 60
1
vote
2
replies
281
views
Gene to use for phylogenic analysis
phylogenic-analysis
updated 4 weeks ago by 45k • written 5 weeks ago by • 0
0
votes
0
replies
158
views
Chrom3D
chrom3d interchromosomal genome model
5 weeks ago by desptsp • 0
0
votes
1
reply
213
views
Scanpy use with reticulate in R : var_group_positions argument set up
R Reticulate Scanpy
5 weeks ago by ZheFrench ▴ 590
1
vote
3
replies
304
views
CPTAC Data analysis
CPTAC proteomics
updated 5 weeks ago by 4.7k • written 5 weeks ago by ▴ 10
78
votes
13
replies
41k
views
10 follow
hg19 Centromere Position and Chromosome Length
centromere ucsc
updated 4 weeks ago by 45k • written 14.6 years ago by ▴ 260
0
votes
3
replies
329
views
How to Process Multiple SRRs for the Same BioSample ?
GEO RNA-seq NCBI miRNAs RNA
updated 5 weeks ago by 150k • written 5 weeks ago by ▴ 40
0
votes
3
replies
315
views
Methylation cpg probes annotation
annotation methylation cpg TCGA
updated 5 weeks ago by 150k • written 5 weeks ago by ▴ 10
1
vote
2
replies
384
views
How to convert .ab1 to fastq
Fastq
updated 5 weeks ago by ▴ 120 • written 5 weeks ago by • 0
0
votes
1
reply
229
views
How to deal with missing annotations in RNASeq data?
eggnogmapper RNASeq
updated 5 weeks ago by ★ 2.9k • written 5 weeks ago by ▴ 140
0
votes
2
replies
272
views
Why protein sequence from AUGUSTUS can't find in blast
genome AUGUSTUS galaxy annotation
4 weeks ago by Jl • 0
1
vote
2
replies
269
views
How to make amazing UMAP to spatialPlot GIF
umap spatial
5 weeks ago by noodlejackson ▴ 40
1
vote
1
reply
211
views
Software for visualizing mass spectromety spectra
MS Mass Spectrometry
updated 4 weeks ago by 22k • written 5 weeks ago by ▴ 40
1
vote
2
replies
308
views
Feedback Wanted: GenAnalyzer - Web App for Protein Sequence Analysis & Mutation Detection
feedback tool
4 weeks ago by genanalyzer24 • 0
1
vote
1
reply
237
views
Detecting Aneuploidy from Bulk RNA-Seq Data
Aneuploidy RNA-Seq
updated 5 weeks ago by 87k • written 5 weeks ago by ▴ 10
0
votes
0
replies
164
views
GSA genome studio call rate calculation issues
Genome GSA studio
5 weeks ago by 1769mkc ★ 1.2k
1
vote
2
replies
414
views
Parsing BAM file per cell from Smart-Seq2 dataset
starsolo star BAM smartseq2 alignment
updated 5 weeks ago by ★ 7.4k • written 5 weeks ago by • 0
0
votes
0
replies
206
views
News: Spring School in Bioinformatics - online, March 31 to April 4
Singularity NGS RNAseq Phylogenomics Docker
5 weeks ago by Physalia-courses ★ 2.6k
2
votes
2
replies
405
views
Gene Expression Timeline Analysis for N=1
Analysis Gene Expression
4 weeks ago by ATRX ★ 1.2k
0
votes
1
reply
552
views
Interactive UMAP for scRNA-seq Data
HTML RMarkdown Interactive-UMAP scRNA-seq
updated 5 weeks ago by • 0 • written 9 weeks ago by • 0
0
votes
0
replies
208
views
Converting PLINK GWAS Summary Statistics (--glm) to BED Format for UCSC Liftover
PLINK LiftOver PLINK2 BED GWAS
5 weeks ago by Mllepnos • 0
3
votes
0
replies
224
views
Tool: PAN-GO Functionome: known functions of all human protein-coding genes
goenrichment function GO goterms geneontology
5 weeks ago by geneontologyhelp ▴ 470
2
votes
1
reply
357
views
How to clarify results from an HLA association analysis - Omnibus tests/HATK/other options
Omnibus HLA HATK GWAS Regression
updated 5 weeks ago by ▴ 20 • written 5 weeks ago by ▴ 50
121,014 results • Page 7 of 2421
Recent Votes
Comment: Why don't I see people calculating FPKM from normalized read counts?
Idat raw data conversion
Idat raw data conversion
A: Illumina BeadArray GTC to VCF conversion
Answer: Analysing gene CNV from TCGA using TCGAbiolinks
Answer: Any recommendation for calculating Fu and Li's D using RStudio?
Answer: Proper preprocessing for ML after limma, quantile normalization and log2 transfo
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Recent Replies
Comment: HOMER Motif Analysis-- homer2 error by Quân • 0
Hi @HypoGG, I have also encountered the same error. I wonder whether you have found the solution for this matter and will you able to share…
Comment: ELISA‑Focused Lab Management & Analysis App – Would You Use It? by GenoMax 150k
> I'm not working with any lab Unless you are closely working with a lab, it would be difficult to produce a product that would be actual…
Comment: ELISA‑Focused Lab Management & Analysis App – Would You Use It? by Novoo • 0
I'm not working with any lab , im just a UG biotech student. That's why im having to go on the internet to ask for every little thing.
Comment: ELISA‑Focused Lab Management & Analysis App – Would You Use It? by Novoo • 0
Oh sorry , I'll keep that in mind.
Comment: ELISA‑Focused Lab Management & Analysis App – Would You Use It? by GenoMax 150k
Please do not post similar content in multiple threads: https://www.biostars.org/p/9611446/ You can keep the discussion limited to a singl…
Comment: Exon-level counts via featureCounts by n_navy • 0
When I use -f parameter, Successfully assigned alignments is being extremely low.
Comment: Why don't I see people calculating FPKM from normalized read counts? by kalavattam ▴ 350
Thank you for correcting me. I've updated the post.
Comment: miRNA alignment and count generation by Jasim • 0
I am also in the same boat bro, i got 000 countfeauture after aligned. After truobleshooting I found that sam file was failed. My sample wa…
Comment: Small‑Lab Data Management & Analytics Tool – What are your biggest pain points? by Mensur Dlakic ★ 29k
My recommendation is to take a couple of days and research what is already available. Is it more productive to spend a week and test severa…
Comment: Running out of disc space with wsl2 by Mensur Dlakic ★ 29k
I think there is a certain requirement for temporary disk space during prefetch, and you are likely blowing through it by running this in p…
Answer: Proper preprocessing for ML after limma, quantile normalization and log2 transfo by Mensur Dlakic ★ 29k
> However, since ML algorithms like KNN, SVM, and NN are sensitive to feature scale and for PCA-based feature extraction, standardization i…
Comment: Why don't I see people calculating FPKM from normalized read counts? by dsull ★ 7.4k
Bo Li and Colin Dewey (the developers of RSEM) introduced TPM in 2009 even before the cufflinks paper introduced FPKM. https://academic.oup…
Comment: Small‑Lab Data Management & Analytics Tool – What are your biggest pain points? by Novoo • 0
Thanks so much for the thoughtful feedback—I really appreciate you laying out the practical challenges. Here’s how I’m addressing each of y…
Comment: Running out of disc space with wsl2 by vladimir_vinarsky • 0
Thank you, I have 32GB rRAM, 16 Cores, Threads 32, and some 120GB on the C:\ drive (which is the SSD). I think the download and processi…
Comment: Filtering vcf file for variants - including non-selected variants by andrebolerbarros • 0
Hey @yokofakun! Thanks for your answer. Unfortunately, this does not seem to work as well... I had to use the variant list with `-T` cri…
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