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545 results • Page 3 of 11
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1
vote
2
replies
215
views
convert a seurat object to expressionset
Seurat
12 days ago by Bine ▴ 60
1
vote
1
reply
170
views
Help/Direction Needed for Data Analysis of RNA
Sequencing RNA-seq DNA-Seq
updated 7 days ago by ★ 5.8k • written 7 days ago by • 0
1
vote
2
replies
1.7k
views
Batch effects and MDSPlot in limma
limma Batch-effect MDS Galaxy
updated 7 days ago by 43k • written 4.8 years ago by • 0
1
vote
2
replies
266
views
Can I readmap short reads to rDNA references?
rDNA assembly
updated 6 days ago by 43k • written 6 days ago by • 0
1
vote
1
reply
815
views
Question for 3 prime bias in rna short read and long read (illumina, ont, pacbio)
rna-seq short-read long-read
updated 18 days ago by 43k • written 11 months ago by ▴ 50
1
vote
1
reply
221
views
Cell type classification using an integrated reference
scRNAseq
updated 22 days ago by ★ 2.3k • written 23 days ago by • 0
1
vote
3
replies
2.0k
views
psmc bootstrapping help
bootstrap psmc
updated 29 days ago by • 0 • written 3.2 years ago by ▴ 50
1
vote
4
replies
381
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics htseq-count RNA-Seq NGS hisat2
updated 10 days ago by ★ 1.7k • written 11 days ago by • 0
1
vote
3
replies
346
views
how to do the repeatability filtering of vcf files?
snp vcf.
updated 22 days ago by 161k • written 23 days ago by • 0
1
vote
1
reply
176
views
Do I need to go back and filter my long-reads?
alignment nanopore filtering QC ONT
updated 8 days ago by 141k • written 8 days ago by ▴ 80
1
vote
1
reply
189
views
Tool for gene function identification
Gene-Function
updated 21 days ago by 43k • written 22 days ago by • 0
1
vote
1
reply
192
views
ComplexHeatmap anno_mark position changes with height of gene expression heatmap
ComplexHeatmap
9 days ago by CTLong ▴ 110
1
vote
0
replies
153
views
DESeq2 comparing timepoints within treatment and account for background control change
RNAseq DEG DESeq2
updated 12 days ago by 43k • written 12 days ago by ▴ 30
1
vote
2
replies
205
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 26 days ago by 43k • written 26 days ago by • 0
1
vote
1
reply
171
views
Failed to download data from EBI with ascp
EBI aspera
updated 12 days ago by 141k • written 12 days ago by ▴ 60
1
vote
2
replies
1.0k
views
An issue with application of SPAdes genome assembly in Galaxy
Galaxy SPAdes
updated 21 days ago by 43k • written 2.4 years ago by • 0
1
vote
4
replies
803
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing wgs
14 days ago by Hyper_Odin ▴ 310
1
vote
1
reply
181
views
R/Python script to collect allele frequency for batch of SNPs in gnomAD database
gnomAD
19 days ago by Shicheng Guo ★ 9.4k
1
vote
1
reply
410
views
Long reads Annotation
long-reads pacbio
updated 18 days ago by 43k • written 2.1 years ago by • 0
1
vote
0
replies
147
views
Contradictions in GSEA results
GSEA Enrichment-analysis PEA
updated 26 days ago by 43k • written 26 days ago by ▴ 30
1
vote
1
reply
472
views
Manta: What does all this mean
manta Variant-calling VEP
updated 21 days ago by 43k • written 9 months ago by • 0
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca ruvseq sva svaseq batch-effect
updated 7 days ago by 43k • written 6.2 years ago by ▴ 40
1
vote
2
replies
279
views
Tumour purity and ploidy estimation
Copy-number Whole-exome-sequencing
7 days ago by bp22 ▴ 80
1
vote
2
replies
255
views
Is it possible to see so little adipocyte in white adipose tissue?
scRNA-seq
27 days ago by kayah • 0
1
vote
3
replies
249
views
CCA with random effects model
CCA
updated 21 days ago by 14k • written 22 days ago by ▴ 120
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq RNA-Seq batch-effect DESeq2
updated 6 days ago by 43k • written 5.1 years ago by ★ 2.6k
1
vote
0
replies
365
views
Differential expression analysis on multiple integrated datasets
microarray Z-score limma differential-gene-expression meta-analysis
updated 14 days ago by 43k • written 2.4 years ago by ▴ 10
1
vote
2
replies
622
views
Nanopore multisample variant calling
SNPs nanopore SNP-calling variants multisample
25 days ago by colindaven 6.4k
1
vote
2
replies
223
views
permutation test in edgeR
rna-seq edgeR
updated 1 day ago by ★ 7.0k • written 15 days ago by • 0
1
vote
3
replies
333
views
Ensembl gene id conversion
biomart ensembl
updated 7 days ago by 82k • written 9 days ago by • 0
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS exome-sequencing batch-effect
updated 5 days ago by 43k • written 6.5 years ago by ▴ 270
1
vote
2
replies
260
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq kallisto
7 days ago by bioinfo ▴ 150
1
vote
2
replies
805
views
What type of normalization does removeBatchEffect function require as the input?
batch limma removeBatchEffect rna-seq batch-effect
updated 7 days ago by 43k • written 21 months ago by ▴ 20
1
vote
1
reply
132
views
Failed kmer content
kmer illumina ngs
updated 14 hours ago by 43k • written 22 hours ago by • 0
1
vote
2
replies
253
views
Deseq generating warning "the model matrix is not full rank"
deseq
updated 28 days ago by ▴ 40 • written 29 days ago by ▴ 40
1
vote
1
reply
218
views
Retrieve a % coverage for each transcript
RNA-seq
updated 6 days ago by 43k • written 6 days ago by ▴ 40
1
vote
1
reply
378
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow python-apollo Apollo
4 days ago by renan.igor • 0
1
vote
2
replies
322
views
BAM to CRAM and BAM recover with smaller size
BAM samtools CRAM
updated 20 days ago by ★ 1.2k • written 5 weeks ago by ▴ 360
1
vote
0
replies
532
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers TRINITY
3 days ago by mathavanbioinfo ▴ 90
1
vote
3
replies
266
views
True variants selection
vcf bcftools
updated 11 days ago by ★ 1.9k • written 12 days ago by • 0
1
vote
0
replies
1.8k
views
Using SVA with RRBS data
sva batch-effect RRBS
updated 7 days ago by 43k • written 7.1 years ago by ▴ 50
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID org.Dr.eg.db
updated 7 days ago by 43k • written 5.5 years ago by ▴ 170
1
vote
0
replies
670
views
Conditions for valid batch effect correction
r batch-effect
updated 7 days ago by 43k • written 5.2 years ago by ▴ 340
1
vote
2
replies
272
views
BWA MEM Alignment mapped small part of the reads!!
bwa mem
updated 28 days ago by ▴ 40 • written 29 days ago by • 0
1
vote
7
replies
882
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19 Mutect2 GATK Variant-Calling
updated 28 days ago by 43k • written 9 months ago by ▴ 100
1
vote
0
replies
117
views
Downloading immne signature and pathway signature genes form publication and KEGG
genes TRANSCRIPTOME_signature
29 days ago by mrazib0210 ▴ 10
1
vote
2
replies
917
views
vg surject for long reads
long-reads vg variation-graph surject
updated 18 days ago by 43k • written 23 months ago by ▴ 10
1
vote
0
replies
183
views
Synthetic lethality and cancer database
interaction lethal synthetic
26 days ago by Shicheng Guo ★ 9.4k
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma sva batch-effect R
updated 8 days ago by 43k • written 3.8 years ago by ▴ 10
1
vote
2
replies
307
views
Extracting information from gff3 file produced by augustus
augustus gff3
updated 8 days ago by 100k • written 10 days ago by • 0
545 results • Page 3 of 11
Recent Votes
Comment: Per base sequence content error in RNAseq analysis
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
Comment: TCGA2STAT Error: Firehose connection
Answer: HaplotypeCaller - only SNPs
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Recent Replies
Comment: How to compare the quality of assemblies by kirillkirilenko ▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by Istvan Albert 100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs by analyst ▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus by atowns21 • 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t by yxwucq • 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error? by Mensur Dlakic ★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks? by HyperEvo • 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus by GenoMax 141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
Comment: some error in building kraken2 database by Art1ess • 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
Comment: TCGA2STAT Error: Firehose connection by LauferVA 4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
Comment: Redirection of Duplicate PMIDs by LauferVA 4.2k
yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus by atowns21 • 0
This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
Answer: HaplotypeCaller - only SNPs by Pierre Lindenbaum 161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
Answer: Gene set enrichment analysis differences between 2020 and 2024 by geneontologyhelp ▴ 380
We have releases about monthly in order to keep our data accurate and reflect current understanding. In 4 years, there have been about 40 r…
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