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184 results • Page 2 of 4
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0
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0
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335
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell Spatial-Transcriptomics
1 day ago by biocellbio • 0
0
votes
8
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334
views
Error in cnetplot enrichplot package
R
updated 5 days ago by 43k • written 5 days ago by • 0
2
votes
3
replies
330
views
How to establish haplotype-specific gene expression levels
RNA-seq Haplotype
updated 1 day ago by ★ 5.9k • written 18 days ago by ▴ 60
1
vote
7
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327
views
gvcf joint calling
WES GATK VCF gVCF
2 hours ago by zihanss • 0
0
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6
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325
views
How to slice a gvcf file with tabix?
Tabix bed gvcf
4 days ago by Sd • 0
0
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7
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325
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 1 day ago by 141k • written 5 days ago by • 0
2
votes
4
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320
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
4 days ago by HyperEvo • 0
0
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5
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318
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 2 days ago by 141k • written 3 days ago by ▴ 90
0
votes
5
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317
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
3 days ago by njornet ▴ 20
2
votes
3
replies
314
views
clustalo - align milions of short seq, memory issue
memory clustalo
updated 5 days ago by ★ 27k • written 5 days ago by ▴ 120
0
votes
5
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313
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
updated 20 hours ago by 100k • written 4 days ago by ▴ 10
2
votes
4
replies
309
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
updated 2 days ago by 43k • written 3 days ago by ▴ 20
2
votes
4
replies
306
views
Should I use unpaired reads from trimmomatic
RNA-seq QC Trimmomatic
updated 4 days ago by 14k • written 5 days ago by • 0
3
votes
4
replies
304
views
Why gatk VariantAnnotator required bam and coverage files
gatk VariantAnnotator
2 days ago by QX • 0
2
votes
5
replies
300
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
2 days ago by Lada ▴ 30
0
votes
0
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288
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome PGAP NCBI roary Prokka
3 days ago by pramach1 ▴ 40
2
votes
4
replies
283
views
interpretartion of a vcf file
calling genotype ONT variant diploid
4 days ago by samuelkalandarov2002 ▴ 10
1
vote
5
replies
282
views
Downsampling fastq file
downsample fastq
updated 5 days ago by 43k • written 5 days ago by ▴ 80
3
votes
5
replies
278
views
Per base sequence content error in RNAseq analysis
RNA-seq analysis
updated 5 days ago by 141k • written 6 days ago by • 0
3
votes
2
replies
277
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni R Statistics p-value Fisher
5 days ago by kristiewyleung • 0
1
vote
2
replies
277
views
PCA plot
DESeq2 PCAplot
updated 2 days ago by 82k • written 3 days ago by ▴ 10
0
votes
0
replies
275
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness IBD GWAS
updated 5 days ago by 43k • written 14 months ago by ▴ 10
7
votes
2
replies
271
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 4 days ago by ▴ 390 • written 5 days ago by • 0
0
votes
3
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269
views
Highest variable features in single cell data
single-cell
updated 1 day ago by ★ 2.4k • written 3 days ago by • 0
0
votes
2
replies
269
views
bam merging for archaic samples
samtools bam
updated 6 days ago by 43k • written 7 days ago by ▴ 100
0
votes
2
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268
views
why renaming Idents in Seurat object doesn't work?
Seurat RenameIdents R
updated 2 days ago by 43k • written 3 days ago by ★ 1.8k
1
vote
3
replies
267
views
some error in building kraken2 database
metagenome kraken2
4 days ago by Art1ess • 0
0
votes
2
replies
264
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment gaps
updated 16 hours ago by ▴ 740 • written 3 days ago by • 0
1
vote
2
replies
259
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign cell-markers
13 hours ago by Francesco ▴ 10
0
votes
1
reply
257
views
absolute path for symbolic links in Snakefile
Snakemake
updated 16 hours ago by ▴ 740 • written 8 days ago by ▴ 60
2
votes
2
replies
255
views
what is the purpose of indexing the reference genome (Kallisto)
indexing Kallisto
updated 1 day ago by ★ 5.9k • written 2 days ago by ▴ 10
0
votes
3
replies
252
views
Difference between samtools "-f 9" and "-f 11"
samtools sam bam
updated 4 days ago by 100k • written 4 days ago by • 0
2
votes
3
replies
251
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
updated 2 days ago by 161k • written 3 days ago by ▴ 30
5
votes
3
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250
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 4 days ago by 141k • written 4 days ago by • 0
1
vote
3
replies
248
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology metagenomics database enzymes genomics
updated 10 hours ago by ★ 27k • written 1 day ago by ▴ 710
0
votes
2
replies
248
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 3 days ago by 43k • written 4 days ago by ▴ 140
2
votes
3
replies
246
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc conda nextflow
updated 17 hours ago by 3.2k • written 1 day ago by ▴ 40
3
votes
3
replies
243
views
Sequence read length shorter than flow cell specification
illumina NGS sequencing
updated 2 days ago by 14k • written 2 days ago by • 0
0
votes
2
replies
241
views
Annovar using R package
Annovar gnomAD R
2 days ago by DKA ▴ 40
1
vote
2
replies
240
views
permutation test in edgeR
rna-seq edgeR
updated 6 days ago by ★ 7.0k • written 20 days ago by • 0
0
votes
2
replies
236
views
BLAST using both nucleotides and taxonomic local databases
blast ncbi taxid taxonomy
updated 2 days ago by 141k • written 2 days ago by ▴ 150
3
votes
3
replies
229
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide Genomic Sequence Uniprot Proteins
updated 5 days ago by 141k • written 6 days ago by ▴ 10
1
vote
3
replies
228
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
5 days ago by WouterDeCoster 47k
0
votes
2
replies
226
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
3 days ago by mropri ▴ 150
3
votes
3
replies
225
views
genome assembly records not present in assembly_summary.txt
ncbi bacteria assembly
updated 1 day ago by 141k • written 2 days ago by ▴ 10
3
votes
1
reply
224
views
Seurat merge and batch correction
Seurat
updated 4 days ago by 43k • written 5 days ago by ▴ 20
0
votes
3
replies
223
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 4 days ago by • 0 • written 5 days ago by • 0
0
votes
2
replies
220
views
Creating Synthetic Sequences for a ML Model
DNA ML
updated 3 days ago by ★ 27k • written 3 days ago by • 0
1
vote
2
replies
219
views
alignment result
RNA-seq samtools hisat2
3 days ago by ahmad.sajad4541 • 0
0
votes
2
replies
218
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 1 day ago by 43k • written 2 days ago by ▴ 10
184 results • Page 2 of 4
Recent Votes
Answer: ChIP-seq datasets: input samples omitted?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
A: Deeptools plotHeatmap - Maintain Order of Input BED file
Comment: NGS forensics: how to know if data is fabricated
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Answer: DNA methylation preprocessing
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Recent Replies
Comment: gvcf joint calling by zihanss • 0
Thanks for your comment, I get it now.
Answer: ChIP-seq datasets: input samples omitted? by ATpoint 82k
In my hands (and from what I know based on many years here) inputs are almost exclusively used during peak calling to correct for loci-spec…
Comment: How to assign cell types after integration in scRNA by ATpoint 82k
No difference here. After all you typically want a label per cluster/group, so either subset to the control condition to do the assignment,…
Comment: Differential Expression using Isoseq-supplemented reference transcriptome by gaoanwei • 0
I found the question and ASK the GPT4 turbo
Answer: Differential Expression using Isoseq-supplemented reference transcriptome by gaoanwei • 0
Your approach seems reasonable and well-informed, though it's perhaps less customary in the field, which could be why you haven't found pap…
Answer: How many reads for WGS Sequencing? by Mensur Dlakic ★ 27k
It takes 29 seconds to assemble this genome (20 CPUs) with the following statistics: 135 contigs, total 2821177 bp, min 200 bp, max …
Comment: NGS forensics: how to know if data is fabricated by noodle ▴ 520
IMO (and unfortunately) there needs to be an effort to develop these algorithms.
Comment: gvcf joint calling by Jeremy Leipzig 22k
the samples that are `./.` have no coverage (or not enough to call a genotype) and the `0/0` are homozygous reference
Answer: How many reads for WGS Sequencing? by GenoMax 141k
Did you download the complete dataset available from ENA/NCBI SRA? This is an older dataset (from 2012) with a total of 1146212 reads and 1…
Comment: When to use .vcf or .gvcf files from GATK HaplotypeCaller? by zihanss • 0
Hello, I want to know that why my gVCF files have "./." besides "0/0", "1/1"? Thanks
Comment: gvcf joint calling by zihanss • 0
![enter image description here][1] [1]: /media/images/15eedc1a-b2c6-4966-be39-b5173dab And I confused with the file that has "./." and…
Comment: gvcf joint calling by zihanss • 0
![enter image description here][1] [1]: /media/images/16fd502c-4e01-4f56-8562-0e0d4aac Okay, this is the merged gVCF file.
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC: by Mensur Dlakic ★ 27k
Enzymes under the umbrella of `1.1.1.-` work `with NAD(+) or NADP(+) as acceptor`. That only tells you about their cofactors, but not about…
Comment: NGS forensics: how to know if data is fabricated by dsull ★ 5.9k
I don't think people have undertaken the effort to create an anomaly detector for RNAseq -- people's efforts are dedicated towards developi…
Comment: NGS forensics: how to know if data is fabricated by dsull ★ 5.9k
I'd say post on pubpeer -- it's the best forum for this sort of discussion. As for what additional analysis I recommend: I'd say look at s…
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