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1,000 results • Page 3 of 20
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6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna RNA-Seq ChIP-Seq
updated 17 days ago by • 0 • written 3.9 years ago by ▴ 120
5
votes
3
replies
320
views
Problems with Nextflow to run NanoRtax Pipeline
NanoRtax Nextflow Nanopore
updated 20 days ago by 6.4k • written 21 days ago by • 0
5
votes
5
replies
847
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq Blacklist
updated 12 days ago by 43k • written 10 months ago by ▴ 30
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
5
replies
535
views
NCBI MEGABLAST versus UCSC BLAT
blast blat alignment megablast
updated 15 days ago by ▴ 510 • written 16 days ago by ▴ 40
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 15 days ago by 43k • written 6.4 years ago by ▴ 10
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 15 days ago by 43k • written 2.7 years ago by ▴ 170
5
votes
3
replies
703
views
Illumina reads preprocessing best practice for snp calling applications
Illumina snp
updated 5 days ago by • 0 • written 9 months ago by ▴ 310
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 22 days ago by 13k • written 15 months ago by ▴ 20
5
votes
4
replies
616
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq EdgeR DEGs DESeq2
6 days ago by BioinfGuru ★ 1.7k
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 4 days ago by 82k • written 5 days ago by ★ 1.7k
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
2
replies
664
views
DESeq2- How to design data for multiple comparisons?
Differential-Gene-Expression RNA-Seq DESeq2 R
updated 15 days ago by 43k • written 3.6 years ago by • 0
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
4
replies
305
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
14
replies
956
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications dorado basecalling nanopore methylation
updated 13 days ago by 141k • written 4 weeks ago by ▴ 20
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
4
replies
613
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
1 day ago by kirillkirilenko ▴ 40
5
votes
5
replies
2.1k
views
batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq tophat batch-effect cufflinks
updated 7 days ago by 43k • written 5.3 years ago by • 0
5
votes
5
replies
5.5k
views
beagle 4 exception: Duplicate marker
vcf IBD plink beagle
updated 29 days ago by 43k • written 9.4 years ago by ▴ 10
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
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 22 days ago by 43k • written 14 months ago by ▴ 50
5
votes
6
replies
391
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot RNAseq Rstudio
updated 22 days ago by 100k • written 23 days ago by • 0
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 6 days ago by 43k • written 9.1 years ago by ▴ 110
5
votes
3
replies
385
views
Ensembl assembly choice for DNA reference with no combined primary assembly
alignment HISAT2 RNA-Seq ensembl Assembly
updated 13 days ago by 141k • written 13 days ago by ▴ 20
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression RNA-seq
updated 15 days ago by 43k • written 6.2 years ago by ▴ 90
5
votes
8
replies
2.3k
views
VariantCalling with single sanger read
snps blast indel Variant-Calling
updated 29 days ago by 43k • written 7.7 years ago by ▴ 70
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 15 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 13 days ago by ★ 2.0k • written 2.8 years ago by ▴ 40
4
votes
3
replies
10k
views
short and long reads
long-reads Assembly short-reads
updated 19 days ago by 43k • written 9.9 years ago by ▴ 290
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq batch-effect DESeq2 Salmon
updated 6 days ago by 43k • written 6.5 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
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
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq batch-effect
updated 7 days ago by 43k • written 4.8 years ago by ▴ 30
4
votes
2
replies
1.2k
views
Tool: Introducing Cramino: a *fast* QC tool for long reads
long-read nanopore pacbio
updated 19 days ago by 43k • written 17 months ago by 47k
4
votes
3
replies
7.4k
views
How to find/decipher Trimmomatic Output
trimmomatic RNA-Seq QC
updated 26 days ago by 43k • written 8.1 years ago by ▴ 110
4
votes
3
replies
7.6k
views
Genotype representation with 0, 1, 2 - what do they mean?
genotype representation phasing imputation gwas
updated 20 days ago by • 0 • written 5.9 years ago by ▴ 180
4
votes
4
replies
390
views
How do I install plink2 on a mac?
plink2 plink
updated 10 days ago by 11k • written 12 days ago by ▴ 10
4
votes
11
replies
481
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 1 day ago by 4.2k • written 2 days ago by • 0
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
5
replies
1.9k
views
which package should be selected for differential gene expression analysis
Differential-gene-expression RNA-Seq
updated 15 days ago by 43k • written 5.5 years ago by ▴ 100
4
votes
7
replies
558
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse JBrowse2
updated 23 days ago by ★ 3.8k • written 26 days ago by ▴ 140
4
votes
2
replies
277
views
Forum: Bioinformatics: Where do I start
Sequencing
updated 8 days ago by 43k • written 8 days ago by ▴ 10
4
votes
1
reply
294
views
Seeking Proper Interpretation of Dispersion Graph: A Call for Statistical and Biological Insight
RNAseq DESeq2 Dispersionplot
updated 25 days ago by 82k • written 25 days ago by • 0
4
votes
3
replies
2.2k
views
The result of differential gene expression analysis should be extracted based on adj.p.value ?
limma microarray bioconductor R
updated 8 days ago by 43k • written 6.3 years ago by ▴ 260
4
votes
3
replies
1.3k
views
GATK best practices for Broad-produced NGS data
NGS GATK4 BroadInstitute Variant-Calling
updated 29 days ago by 43k • written 5.4 years ago by ▴ 30
4
votes
4
replies
463
views
Why number of interactions decreased in current string database for plasmodium
string interactions ppi
updated 13 days ago by ▴ 70 • written 13 days ago by ▴ 840
4
votes
4
replies
329
views
How to fetch published paper of a BioProject
BioProject pumbed NGS
15 days ago by Morteza • 0
4
votes
5
replies
528
views
Getting refseq assembly accession numbers from list of species names
haystac accession refseq assembly ncbi
updated 20 days ago by 141k • written 20 days ago by • 0
1,000 results • Page 3 of 20
Recent Votes
Answer: Figures are disappeared from html report of SnpEff
Comment: How to trim transcripts using information from NCBI contamination screen report
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
A: What is the VEP Impact column?
is oxford nanopore technology data paired or single end sequencing?
is oxford nanopore technology data paired or single end sequencing?
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Recent Replies
Comment: Figures are disappeared from html report of SnpEff by Pierre Lindenbaum 161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files by Pierre Lindenbaum 161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
Comment: Figures are disappeared from html report of SnpEff by analyst ▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data by Kazo • 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work? by Assa Yeroslaviz ★ 1.8k
I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
Answer: Finding orthologs between genome error by Adrian Altenhoff ★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid by ashaneev07 ▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM by dsull ★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data by sehriban.buyukkilic ▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data by sehriban.buyukkilic ▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file by Pierre Lindenbaum 161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file by Maria • 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff by Pierre Lindenbaum 161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
Comment: Fetch table from clinvar database according to a list of rsid by Pierre Lindenbaum 161k
ah ! and your code doesn't work because clinvar ID is not a rs-ID.
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