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1,000 results • Page 1 of 20
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20
votes
17
replies
3.2k
views
How to add "transcript" feature to a gtf file?
gtf
updated 9 months ago by ★ 1.2k • written 3.2 years ago by ▴ 110
15
votes
16
replies
1.7k
views
ncbi error report log for validate fastq issue
sra-tools
updated 6 months ago by 141k • written 6 months ago by ★ 1.2k
14
votes
10
replies
902
views
How to remove center population from seurat cluster
single-cell
4 months ago by synat.keam ▴ 100
14
votes
18
replies
2.2k
views
Clustering in single cell
seurat single-cell
updated 6 months ago by ▴ 200 • written 6 months ago by ▴ 260
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch-effect
updated 7 days ago by 43k • written 6.8 years ago by ★ 1.3k
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 14 days ago by 43k • written 5.0 years ago by ▴ 260
10
votes
15
replies
1.8k
views
Can't find a variant which suppose must have in a vcf file
variant-calling bcftools nf-core
10 months ago by Chris ▴ 260
10
votes
14
replies
4.9k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig read-length deeptools ATAC-seq
updated 10 months ago by 43k • written 4.2 years ago by ▴ 50
10
votes
6
replies
970
views
RNA seq, secreted protein
protein gene secreted
updated 8 months ago by 21k • written 16 months ago by ▴ 170
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database analysis ontology pathway
updated 10 months ago by 43k • written 8.0 years ago by ▴ 330
9
votes
5
replies
479
views
Annotation of Complex Heatmap
complexheatmap
12 weeks ago by abiuma ▴ 30
9
votes
15
replies
1.3k
views
Construction of single sequence assembly out of contigs
Contigs Bacteria Genome WGS
4 months ago by analyst ▴ 20
9
votes
13
replies
15k
views
Sort bam file by coordinates using samtools
next-gen-sequencing gene rna-seq
updated 10 months ago by 43k • written 5.6 years ago by ▴ 30
9
votes
5
replies
713
views
Prophage prediction tool
prophage PHASTER prediction
updated 9 months ago by 141k • written 9 months ago by ▴ 160
8
votes
5
replies
1.9k
views
BLASTp command line : filtering results by a minimum % of identity and % coverage
BLASTp
updated 7 months ago by 43k • written 2.5 years ago by ▴ 160
8
votes
10
replies
688
views
bash script
whole-genome-sequencing
updated 8 days ago by 43k • written 15 days ago by ▴ 30
8
votes
7
replies
548
views
adjusting parameters in ViolinPlot did not work
single-cell
updated 10 weeks ago by 43k • written 10 weeks ago by ▴ 100
8
votes
6
replies
907
views
How to create a Venn Diagram for overlapping SVs from a merged VCF
truvari structural-variants r vcf venn-diagram
5 months ago by Matteo Ungaro ▴ 100
8
votes
5
replies
811
views
Frustrated with DEA results
microarray differential-expression
updated 6 months ago by ★ 5.8k • written 6 months ago by • 0
8
votes
7
replies
1.0k
views
Why does Ensembl VEP provide HGVSg for some variants and not others?
vcf VEP
10 months ago by Jeremy Leipzig 22k
8
votes
10
replies
2.0k
views
PyWGCNA
WGCNA
10 months ago by yoshifumimiya ▴ 40
7
votes
7
replies
4.9k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines DESeq2 time-series RNA-Seq
updated 10 months ago by 43k • written 5.3 years ago by ▴ 80
7
votes
6
replies
1.3k
views
On "wings" in volcano plots...
DEG volcano DGE statistics DE
updated 11 months ago by 82k • written 11 months ago by ▴ 190
7
votes
7
replies
568
views
6 follow
PCA plot interpretation (single population)
PCA GWAS pruning
11 weeks ago by Shane ▴ 20
7
votes
12
replies
1.6k
views
How to pass arguments in a bash script to perform read alignment to the reference?
exome bwa bash
updated 5 months ago by 43k • written 4.2 years ago by ▴ 310
7
votes
13
replies
4.4k
views
6 follow
Is trimming necessary for RNAseq?
RNA-Seq trimming fastqc
updated 5 months ago by 82k • written 3.4 years ago by ▴ 10
7
votes
8
replies
8.9k
views
Determining read count
trimmomatic rna-seq trinity
updated 8 months ago by 43k • written 8.0 years ago by ▴ 110
7
votes
8
replies
4.2k
views
DEseq2 design matrix with 3 factors
RNA-seq deseq2
updated 10 months ago by 43k • written 3.9 years ago by ▴ 60
7
votes
13
replies
936
views
deal with PCA and my samples
PCA DEG meta-analysis
5 months ago by ali • 0
7
votes
7
replies
1.9k
views
Sort and convert the SAM files to BAM
samtools RNA-seq NGS
updated 8 months ago by 43k • written 5.7 years ago by ▴ 40
7
votes
3
replies
1.6k
views
What are the best tools for Genome assembly
Assembly genome
updated 10 months ago by 43k • written 5.7 years ago by ▴ 10
7
votes
9
replies
1.1k
views
Calculation of TMB on gene level
genomics
updated 7 months ago by ▴ 680 • written 7 months ago by ▴ 20
6
votes
3
replies
2.0k
views
Gene network with expression data
network RNA-Seq
updated 10 months ago by 43k • written 6.4 years ago by ▴ 30
6
votes
7
replies
1.8k
views
Reference genome for RNA-Seq reads decontamination
FastQ_Screen RNA-Seq
updated 8 months ago by 43k • written 4.1 years ago by ▴ 70
6
votes
8
replies
1.2k
views
conda: command not found: gatk.
conda gatk
10 months ago by bestone ▴ 30
6
votes
5
replies
682
views
Log2 transformation is well used, but is there a good paper that can be used as reference ?
TPM log2-transformation r
updated 3 months ago by 87k • written 3 months ago by ▴ 140
6
votes
2
replies
725
views
miRNA tool for search targets for genes
mirna targets
updated 10 months ago by 43k • written 2.8 years ago by ★ 1.2k
6
votes
6
replies
760
views
extract the original sequence from multiple sequence alignment (MSA)
MSA alignment
4 months ago by Ann ▴ 40
6
votes
5
replies
466
views
IGV signal visualization, low and high signals
ATAC-seq IGV
updated 8 weeks ago by 100k • written 8 weeks ago by ▴ 30
6
votes
5
replies
747
views
merging replicates
ChIP-seq
updated 4 months ago by 82k • written 4 months ago by • 0
6
votes
9
replies
2.0k
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM Bowtie
updated 11 months ago by 43k • written 15 months ago by ▴ 50
6
votes
3
replies
544
views
Optimal Over Representation Analysis DE genes foldFC threshold?
ClusterProfiler ORA EnrichGo DGE
updated 9 months ago by 4.2k • written 9 months ago by ▴ 100
6
votes
2
replies
838
views
Can the input file name be the same as the output file in `samtools sort`?
Samtools
updated 10 months ago by 43k • written 2.2 years ago by ▴ 180
6
votes
1
reply
445
views
16S vs shotgun tools
metagenomics
8 months ago by anasjamshed ▴ 120
6
votes
7
replies
561
views
NF-Core ampliseq - Rscript markdown error
nf-core ampliseq
updated 3 months ago by 54k • written 3 months ago by • 0
6
votes
3
replies
629
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics box-plot R scale_adjustment logarithm
updated 4 months ago by ▴ 880 • written 4 months ago by ▴ 40
6
votes
4
replies
6.5k
views
What is gnomAD allele frequency
AF gnomAD
updated 3 months ago by ▴ 760 • written 3.0 years ago by ▴ 50
6
votes
12
replies
2.0k
views
Help with error in cellranger
Cellranger
updated 11 months ago by 141k • written 11 months ago by ▴ 260
6
votes
5
replies
707
views
Tests for the linear and non-linear relationship between two genes
ode drc correlation regression rnaseq
updated 3 months ago by 82k • written 3 months ago by ▴ 40
6
votes
9
replies
2.9k
views
How to analyze the scRNA seq Fastq files from NCBI
SRAtool Cellranger NCBI
updated 10 months ago by 43k • written 2.3 years ago by ▴ 20
1,000 results • Page 1 of 20
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: 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…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by GenoMax 141k
Let us know when you find out. Would be a useful thing to know what the data looks like.
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