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1,000 results • Page 3 of 20
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5
votes
4
replies
617
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
1 day ago by kirillkirilenko ▴ 40
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 7 days ago by 43k • written 9.1 years ago by ▴ 110
5
votes
2
replies
665
views
DESeq2- How to design data for multiple comparisons?
Differential-Gene-Expression RNA-Seq DESeq2 R
updated 16 days ago by 43k • written 3.6 years ago by • 0
5
votes
4
replies
2.2k
views
How do we process Kallisto output (continuous real values) for DESEQ2 analysis (which strictly require discrete count values)?
read-counts DESEQ2 differential-gene-expression kallisto
updated 16 days ago by 43k • written 2.7 years ago by ▴ 170
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq breast cancer subtyping
updated 8 days ago by ▴ 70 • written 5.7 years ago by ▴ 50
5
votes
2
replies
1.0k
views
How to perform batch correction when we have only single condition?
sva combat batch-effect DESeq2
updated 8 days ago by 43k • written 3.8 years ago by ▴ 680
5
votes
4
replies
620
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq EdgeR DEGs DESeq2
7 days ago by BioinfGuru ★ 1.7k
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 16 days ago by 43k • written 6.5 years ago by ★ 1.6k
5
votes
13
replies
9.1k
views
8 follow
biomaRt: Timeout on getBM().
r biomart ensembl
updated 14 days ago by ★ 2.0k • written 2.8 years ago by ▴ 40
5
votes
3
replies
1.0k
views
How to normalize long-read RNA-seq data for comparison with short-reads
RNAseq long-reads normalization short-reads
updated 23 days ago by 13k • written 15 months ago by ▴ 20
5
votes
3
replies
704
views
Illumina reads preprocessing best practice for snp calling applications
Illumina snp
updated 6 days ago by • 0 • written 9 months ago by ▴ 310
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov scatter-plot anova
updated 8 days ago by 43k • written 3.2 years ago by ▴ 170
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq batch batch-effect sequencing
updated 8 days ago by 43k • written 2.9 years ago by ▴ 60
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 14 days ago by • 0 • written 3.8 years ago by ★ 1.8k
5
votes
4
replies
307
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger scRNA-seq 10x
9 days ago by Spring • 0
5
votes
3
replies
317
views
Best genome browser for manual curation of gene structure(s)?
structure gene
updated 13 days ago by ★ 3.8k • written 14 days ago by ★ 5.3k
5
votes
12
replies
1.5k
views
Subbmission Data
RNA-seq
updated 23 days ago by 43k • written 14 months ago by ▴ 50
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression RNA-seq
updated 16 days ago by 43k • written 6.2 years ago by ▴ 90
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 16 days ago by 43k • written 6.4 years ago by ▴ 10
5
votes
13
replies
1.1k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 5 days ago by 82k • written 6 days ago by ★ 1.7k
5
votes
5
replies
538
views
NCBI MEGABLAST versus UCSC BLAT
blast blat alignment megablast
updated 16 days ago by ▴ 510 • written 17 days ago by ▴ 40
5
votes
5
replies
848
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq Blacklist
updated 13 days ago by 43k • written 10 months ago by ▴ 30
5
votes
3
replies
385
views
Ensembl assembly choice for DNA reference with no combined primary assembly
alignment HISAT2 RNA-Seq ensembl Assembly
updated 14 days ago by 141k • written 14 days ago by ▴ 20
5
votes
6
replies
392
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot RNAseq Rstudio
updated 23 days ago by 100k • written 24 days ago by • 0
5
votes
3
replies
321
views
Problems with Nextflow to run NanoRtax Pipeline
NanoRtax Nextflow Nanopore
updated 21 days ago by 6.4k • written 22 days ago by • 0
5
votes
14
replies
961
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications dorado basecalling nanopore methylation
updated 14 days ago by 141k • written 5 weeks ago by ▴ 20
5
votes
5
replies
2.1k
views
batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq tophat batch-effect cufflinks
updated 8 days ago by 43k • written 5.3 years ago by • 0
4
votes
2
replies
1.7k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF SAM BAM GFF minimap2
updated 8 days ago by ▴ 130 • written 12 months ago by • 0
4
votes
11
replies
495
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 1 day ago by 4.2k • written 2 days ago by • 0
4
votes
4
replies
394
views
How do I install plink2 on a mac?
plink2 plink
updated 10 days ago by 11k • written 13 days ago by ▴ 10
4
votes
5
replies
350
views
merging tetraploid vcf files through bcftools
vcf bcftools
24 days ago by analyst ▴ 30
4
votes
2
replies
1.2k
views
Tool: Introducing Cramino: a *fast* QC tool for long reads
long-read nanopore pacbio
updated 20 days ago by 43k • written 17 months ago by 47k
4
votes
4
replies
355
views
Bowtie2 mapping is slow
metagenomics bowtie2 mapping read
updated 13 days ago by 6.4k • written 22 days ago by • 0
4
votes
6
replies
1.4k
views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlength…
gff3 GenomicRanges ORFik GenomicFeatures
updated 10 days ago by 141k • written 15 months ago by ▴ 30
4
votes
2
replies
316
views
Assume "yes" as the answer to any prompts with bioconda
docker container bioconda
updated 7 days ago by 8.5k • written 7 days ago by ▴ 20
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq batch-effect
updated 8 days ago by 43k • written 4.8 years ago by ▴ 30
4
votes
11
replies
1.3k
views
Paired layout, but one fastq file
fastq
updated 28 days ago by 141k • written 13 months ago by ▴ 120
4
votes
2
replies
278
views
Forum: Bioinformatics: Where do I start
Sequencing
updated 9 days ago by 43k • written 9 days ago by ▴ 10
4
votes
7
replies
4.5k
views
snakemake output directory
snakemake ngs
updated 9 days ago by • 0 • written 3.9 years ago by ▴ 200
4
votes
3
replies
10k
views
short and long reads
long-reads Assembly short-reads
updated 20 days ago by 43k • written 9.9 years ago by ▴ 290
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq countOverlaps R
updated 8 days ago by 43k • written 6.3 years ago by ★ 1.9k
4
votes
4
replies
461
views
Error Codes in Snakemake
python snakemake
19 days ago by 888pea ▴ 10
4
votes
4
replies
14k
views
Heatmap with custom gene labels annotated on the rows
differential-gene-expression RNAseq heatmap
updated 16 days ago by 43k • written 4.7 years ago by ▴ 370
4
votes
7
replies
591
views
UK biobank versus Genomics England
WGS DRAGEN GenomicsEngland UK-BRAP vcf
written 12 weeks ago by ★ 4.3k
4
votes
6
replies
832
views
bwa mem hangs after a few thousand reads
bwa alignment variant-calling bwa-mem
updated 23 days ago by 43k • written 4 months ago by ▴ 30
4
votes
4
replies
405
views
Problem generating paired end reads when converting Cell Ranger's BAM result to FASTQ
fastq bam
26 days ago by ntuzov • 0
4
votes
2
replies
226
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa samtools mapping genome
updated 21 days ago by 161k • written 21 days ago by • 0
4
votes
13
replies
864
views
RNAseq of primary tumor and metastases in two different organ
metastases RNA-seq DEG R
updated 8 days ago by ★ 1.7k • written 14 days ago by • 0
4
votes
7
replies
385
views
To get p-values for the TPM
P-value TPM RSEM
updated 12 hours ago by ★ 5.8k • written 1 day ago by • 0
4
votes
9
replies
1.1k
views
Error in openning FastQC
fastqc igv
updated 27 days ago by 141k • written 8 months ago by • 0
1,000 results • Page 3 of 20
Recent Votes
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
Detecting somatic variants in non-tumor tissue without normals
Answer: Sequence read length shorter than flow cell specification
Answer: Sequence read length shorter than flow cell specification
Comment: Why gatk VariantAnnotator required bam and coverage files
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
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Recent Replies
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Ram 43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
Comment: Annovar using R package by DKA ▴ 40
Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
Comment: Treatment VS Control in Single Cell RNAseq analysis by ATpoint 82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets by ATpoint 82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
Comment: Why gatk VariantAnnotator required bam and coverage files by QX • 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis by kilcdincer ▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases by GenoMax 141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases by 5heikki 11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
Answer: why renaming Idents in Seurat object doesn't work? by Bioinfotec ▴ 10
I think when you give indent to seuObj : Idents(seuObj) <- 'RNA_snn_res.0.1' You may wrongly assign other value to it such as …
Answer: ScRNAseq-How to correctly choose cell type marker genes by Bioinfotec ▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question by Bioinfotec ▴ 10
In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
Comment: Sequence read length shorter than flow cell specification by GenoMax 141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing by rohitsatyam102 ▴ 850
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification by ATpoint 82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
Comment: Why gatk VariantAnnotator required bam and coverage files by Pierre Lindenbaum 161k
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator : VariantAnnotator …
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