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120,854 results • Page 3 of 2418
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0
votes
3
replies
302
views
Higher number of reads mapped to transcriptome vs genome in star mapping
riboseq star bam transcriptome alignment
updated 11 days ago by 21k • written 11 days ago by • 0
1
vote
4
replies
486
views
Visualisation of read depth
coverage read-depth variant-calling
updated 10 days ago by 45k • written 11 days ago by • 0
7
votes
5
replies
801
views
Tool: AliNe (Alignment in Nextflow)
nextflow alignment
11 days ago by Juke34 9.2k
0
votes
0
replies
224
views
construct PKN
REGULATORY PKN MOUSE NETWORKS GENE
11 days ago by rahma.khoualdia • 0
3
votes
5
replies
466
views
Tool for automatic immune cell annotation in MOUSE?
immune single-cell annotation
6 days ago by txema.heredia ▴ 210
4
votes
12
replies
7.1k
views
12 follow
How to draw venn diagram for two CNV lists?
venn
updated 11 days ago by 11k • written 10.3 years ago by ▴ 480
0
votes
2
replies
285
views
merging diploid and tetraploid vcfs
bcftools diploid tetraploid
11 days ago by analyst ▴ 60
0
votes
1
reply
248
views
TMM normalized CPM
TPM CPM TMM
updated 10 days ago by 87k • written 11 days ago by ▴ 20
0
votes
0
replies
178
views
Normlizatiom in DiffBind
DiffBind CHIP-Seq
11 days ago by Siqi • 0
0
votes
1
reply
235
views
Obtain genome coordinates for a DNA sequence using ENSEMBL API
Ensembl API
updated 11 days ago by 150k • written 11 days ago by • 0
0
votes
0
replies
198
views
Forum: Decoding Corvid Intelligence: Genomics, AI & the Genetics of Cognition
neurogenetics comparative-genomics bioinformatics genomics machine-learning
updated 11 days ago by 45k • written 11 days ago by • 0
3
votes
5
replies
477
views
GBWT Construction Error: "Sources X and Y both have node Z" When Building GBZ from GFA
vg
updated 8 days ago by ▴ 610 • written 11 days ago by ▴ 20
8
votes
16
replies
766
views
6 follow
prokka with too many "hypothetical proteins" and genome comparison
comparison genome galaxy prokka
11 days ago by avinci1 ▴ 20
0
votes
1
reply
270
views
Split paired ended hWGS FASTq files to simulate difference sequence coverage
whole-genome-sequencing wgs FASTQ coverage
updated 12 days ago by ★ 1.5k • written 12 days ago by ▴ 20
1
vote
11
replies
660
views
OMA use case
oma omastandalone
updated 6 days ago by 150k • written 12 days ago by • 0
0
votes
0
replies
194
views
News: Machine Learning for Longitudinal Data with Python – Online Course (6-9 May)
MachineLearning LongitudinalData DeepLearning Omics
12 days ago by Physalia-courses ★ 2.6k
1
vote
2
replies
431
views
Recommended workflow to pre-process and demultiplex scRNAseq data based on the HTOs and ADTs
ADT HTO demultiplexing scRNAseq
updated 12 days ago by 150k • written 12 days ago by • 0
0
votes
3
replies
289
views
bwa-mem keeps failing to locate the index files
bwa bwa-mem
updated 12 days ago by 87k • written 12 days ago by ▴ 30
1
vote
5
replies
440
views
6 follow
Efficient Gene Prediction on Large Eukaryotic Genomes
tools prediction gene
updated 12 days ago by 22k • written 14 days ago by • 0
0
votes
0
replies
153
views
Olink - OlinkAnalyze Package - olink_umap_plot function
Olink proteomics
12 days ago by kristina • 0
3
votes
0
replies
204
views
Herald: The Biostar Herald for Wednesday, March 19, 2025
herald
12 days ago by Biostar 3.4k
0
votes
0
replies
160
views
Cosmic database update issue in annovar
annovar cosmic genomics
updated 12 days ago by 45k • written 12 days ago by • 0
1
vote
1
reply
330
views
Transforming diploid GT on male X and Y chromosome to haploid
VCF genotype gVCF
12 days ago by Michaela ▴ 10
3
votes
2
replies
299
views
How do I figure out pangenome location of hg38 coordinates?
pangenome hg38 vg
12 days ago by a5864557 ▴ 10
5
votes
7
replies
521
views
How I can curate all exon start-end positions for 50 genes (to create GTF file)?
gtf curation gene
updated 11 days ago by 150k • written 13 days ago by ▴ 10
0
votes
0
replies
158
views
generating manhattan plot through hail
plot manhattan hail visualizations gwas
12 days ago by nitya • 0
0
votes
0
replies
154
views
Hard Filtering Differences between WES and WGS
WES WGS Hard-Filtering
updated 12 days ago by 45k • written 12 days ago by • 0
0
votes
3
replies
306
views
Am I accounting for replicates correctly in pseudobulk analysis?
deseq2 single-cell pseudobulk
updated 12 days ago by 87k • written 12 days ago by ▴ 370
2
votes
4
replies
435
views
Is there too little variation to detect meaningful gene changes?
DESEQ
updated 12 days ago by 102k • written 14 days ago by ▴ 50
3
votes
5
replies
406
views
nanopore SNV callers returns empty VCF
snv_caller nanopore
updated 6 days ago by 102k • written 12 days ago by ▴ 10
15
votes
3
replies
1.2k
views
Tutorial: Avoiding the Pitfalls of the Anaconda License: A Practical Guide
conda Anaconda license
12 days ago by Juke34 9.2k
0
votes
2
replies
254
views
How many cells are needed in subcluster to draw conclusions?
immunology T-cells scRNA-seq
11 days ago by S • 0
0
votes
1
reply
203
views
Question about assigning gene names, tximport and DESeq2
tximport deseq2
updated 12 days ago by 102k • written 13 days ago by ▴ 150
3
votes
3
replies
344
views
RNASeq: Confused about adapters with barcodes and seq company's filtering
atria rnaseq adapter-trimming
updated 11 days ago by 150k • written 13 days ago by • 0
1
vote
2
replies
276
views
VEP won't show symbols for all variants; SnpEff will, but won't for others
vep snpeff
updated 13 days ago by 23k • written 14 days ago by ▴ 20
0
votes
2
replies
221
views
How to plot LMER estimate values in heatmap ?
cell scRNAseq TF lmer transcription
12 days ago by carolofharvest ▴ 50
1
vote
2
replies
1.2k
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
13 days ago by ecSeq Bioinformatics ▴ 10
0
votes
1
reply
197
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
tehnical-replicates DESeq2 RNA-Seq
updated 13 days ago by 45k • written 13 days ago by • 0
0
votes
3
replies
297
views
Can anyone help me download the dbSNP data for Bos taurus ARS-UCD1.3?
GWAS genetics WGS
updated 10 days ago by 45k • written 13 days ago by • 0
0
votes
1
reply
219
views
Co-expression analysis of miRNAs and target mRNAs
miRNA targets co-expression miRNA-mRNA
updated 13 days ago by 21k • written 14 days ago by ▴ 40
0
votes
0
replies
158
views
Beagle Imputation
Beagle Imputation
14 days ago by mahlet.teka • 0
0
votes
0
replies
270
views
Issue with bam-readcount and fpfilter.pl: Saying "failed to get readcounts for variant allele"
bam-readount somaticsniper
updated 14 days ago by 165k • written 14 days ago by • 0
2
votes
2
replies
274
views
miRNA-seq: QC reports and workflow
miRNA-seq ION-Torrent RNA-seq FASTQC
12 days ago by omicon ▴ 40
1
vote
0
replies
147
views
How to Run Large-Scale Foldseek Comparisons (Human vs. C. elegans)
c.elegans Foldseek Genes Orthologs Homologs
14 days ago by bioinformatics_rk ▴ 10
0
votes
1
reply
241
views
Recommendations for Reference-guided de novo assembly assembly approaches or pipelines?
ont assembly wgs nanopore genomics
updated 14 days ago by ★ 1.5k • written 15 days ago by ▴ 30
0
votes
1
reply
215
views
Per Base Sequence Content FastQC
RNA-seq quality-control
updated 14 days ago by ★ 1.5k • written 14 days ago by ▴ 20
3
votes
2
replies
333
views
Seeking Advice on Handling Multiple Datasets for Differential Analysis in Transcriptomics
Data-Integration Differential-Analysis Transcriptomics Data-Normalization
13 days ago by Riley J • 0
2
votes
3
replies
296
views
Population genetics with mutect2 data
haplotypecaller mutect2
updated 12 days ago by 4.6k • written 14 days ago by • 0
1
vote
2
replies
243
views
ggplot of two data set with different colors
geom_line scale_colour_manual ggplot2
updated 14 days ago by • 0 • written 14 days ago by ▴ 60
1
vote
2
replies
253
views
Gene to use for phylogenic analysis
phylogenic-analysis
updated 14 days ago by 45k • written 14 days ago by • 0
120,854 results • Page 3 of 2418
Recent Votes
Good QC Package (RSeQC or alternative) for Salmon mapping/quantification results?
Comment: rRNA depletion of RIP-seq samples
Comment: rRNA depletion of RIP-seq samples
Comment: rRNA depletion of RIP-seq samples
Answer: Parsing BAM file per cell from Smart-Seq2 dataset
CNVkit reference.cnn .cnr .cns log ratio
A: CNVkit reference.cnn .cnr .cns log ratio
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Recent Replies
Comment: Lacking exons in gtf file of a virus' genome by GenoMax 150k
Since the host is always going to be there you can do the mapping to a combined three transcriptome pool, as a test/first-pass. That will g…
Comment: Good QC Package (RSeQC or alternative) for Salmon mapping/quantification results by squidqid • 0
Did you ever get an answer to this question?
Comment: Lacking exons in gtf file of a virus' genome by ZuelTech • 0
I mean, can I map all lists of the libraries ( HAZV-infected, LGTV-infected, uninfected) to the HAZV genome? Can I also map them to the LGT…
Comment: Lacking exons in gtf file of a virus' genome by GenoMax 150k
> Then, I want to map the libraries to each of the virus genome. Is this possible? Possible but will that be logical. If you have all thr…
Comment: Lacking exons in gtf file of a virus' genome by ZuelTech • 0
Thank you! Btw, going back to mapping, I’m working with a vector infected with HAZV and LGTV virus. I have libraries with the host infected…
Comment: Lacking exons in gtf file of a virus' genome by Michael 55k
Yes, that you can do as well. Then you don't need to use STAR. But I would add the host transcriptome as a decoy there.
Comment: Lacking exons in gtf file of a virus' genome by ZuelTech • 0
I see, thank you so much! I’ll try this method. Can I also use Salmon in quantification?
Comment: Lacking exons in gtf file of a virus' genome by Michael 55k
> Does it mean I don’t need to put a gtf file when I do mapping to HAZV > genome? Indeed, unless you want to generate the count file in ST…
Comment: Lacking exons in gtf file of a virus' genome by ZuelTech • 0
Thank you! I’m new to bioinformatics, particularly on working with virus. What can you recommend on what to do with mapping with the reads …
Comment: Lacking exons in gtf file of a virus' genome by ZuelTech • 0
Thank you. But I think the one you provided is from Refseq (as evident from the file name “GCF…”, mine I used the genome from GenBank with …
Answer: Lacking exons in gtf file of a virus' genome by Michael 55k
If there are no exons, that means that the annotators didn't consider splicing relevant. This is common for bacteria and viruses. Therefore…
Comment: Lacking exons in gtf file of a virus' genome by GenoMax 150k
You can find the GTF file here --> https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/831/085/GCF_002831085.1_ASM283108v1/ Be sure to get th…
Comment: Lacking exons in gtf file of a virus' genome by ZuelTech • 0
No transcriptome available. I'm particularly using a virus genome. I need to perform indexing and mapping using STAR. Is there a way to kno…
Comment: Lacking exons in gtf file of a virus' genome by ATpoint 87k
If no proper annotations are present in terms of GTF, is there a transciptome fasta available? Then you could quantify with something like …
Comment: Reannotation of complete bacterial genome sequence by Juke34 9.2k
You may use [Bactopia](https://github.com/bactopia/bactopia)
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