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41
votes
55
replies
13k
views
6 follow
hash function for DNA sequences
hash hashing DNA
8.6 years ago by midox ▴ 290
28
votes
17
replies
23k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
2.9 years ago by Leite ★ 1.3k
25
votes
25
replies
8.7k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq beta diversity metagenomics
4.3 years ago by dpc ▴ 250
23
votes
22
replies
54k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink vcf fam gatk vcftools
updated 23 months ago by • 0 • written 6.5 years ago by ▴ 270
23
votes
10
replies
6.1k
views
How to predict individual ethnicity information by using hapmap data
SNP Ethnicity Hapmap
updated 3.5 years ago by 88k • written 6.7 years ago by ▴ 40
22
votes
20
replies
2.8k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast RNA-Seq genome gene
updated 19 months ago by 44k • written 8.3 years ago by ★ 3.4k
22
votes
19
replies
3.5k
views
targets of a list of miRNAs
miRNAs RNA-Seq DEanalysis target-prediction
8.1 years ago by zizigolu ★ 4.3k
20
votes
17
replies
6.5k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein filtering bbmap bbduk phix
7.2 years ago by Anand Rao ▴ 640
20
votes
17
replies
4.0k
views
How to add "transcript" feature to a gtf file?
gtf
updated 16 months ago by ★ 1.2k • written 3.7 years ago by ▴ 110
20
votes
15
replies
31k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 2.3 years ago by 44k • written 8.8 years ago by ▴ 200
19
votes
43
replies
6.5k
views
Annotation of huge number of CNV files
CNV annotation TCGA
6.2 years ago by nazaninhoseinkhan ▴ 530
18
votes
7
replies
1.7k
views
How to calculate if statistically a variable of a bulk RNA-seq affects the comparison of interest?
DESeq2 Variable RNA-seq
2.1 years ago by Rafael Soler ★ 1.3k
18
votes
19
replies
2.6k
views
6 follow
Extremely important marker gene has many reads based on IGV viewer but no quantified reads
rna-seq sequencing igv alignment next-gen
updated 23 months ago by 44k • written 5.8 years ago by • 0
18
votes
4
replies
9.0k
views
How To Find Rna-Seq Data Of Published Papers?
geo next-gen RNA-seq
updated 20 months ago by 44k • written 11.2 years ago by ▴ 950
18
votes
19
replies
3.2k
views
Sorting sequences according header
software error sequence Assembly next-gen
8.2 years ago by Gian77 ▴ 70
17
votes
37
replies
5.4k
views
No alias or index file found for protein database
next-gen software error sequence
updated 5.4 years ago by 20 • written 5.6 years ago by ▴ 530
17
votes
8
replies
2.6k
views
Number of unique authors in PubMed in last 10 years
PubMed
8.6 years ago by nejc ▴ 50
17
votes
13
replies
7.1k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment genome sequencing
7.5 years ago by lghust2011 ▴ 110
16
votes
10
replies
6.0k
views
6 follow
Powerful desktop computer for genomics
next-gen sequencing ChIP-Seq RNA-Seq
8.4 years ago by Alternative ▴ 290
16
votes
16
replies
3.5k
views
Using DESeq2 results for building a classifier
deseq2 RNA-Seq differentially expressed genes
6.6 years ago by bioinfo456 ▴ 150
16
votes
21
replies
2.6k
views
Why there are different hit for a same gene in different species
gene blast ortholog paralog
8.1 years ago by Farbod ★ 3.4k
16
votes
38
replies
18k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 2.5 years ago by 44k • written 9.7 years ago by ▴ 920
16
votes
17
replies
3.5k
views
6 follow
RNA seq pipeline
RNA-Seq
7.0 years ago by dimitrischat ▴ 210
16
votes
14
replies
18k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters trimmomatic RNA-seq
6.4 years ago by salamandra ▴ 550
16
votes
18
replies
6.0k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
15
votes
14
replies
3.6k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq bwa mem bowtie2 alignment
6.8 years ago by John ▴ 270
15
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 6 months ago by 44k • written 7.3 years ago by ★ 1.4k
15
votes
19
replies
2.1k
views
trimmomaric command for a fasta file?
trimmomatic
updated 6.5 years ago by 44k • written 6.5 years ago by • 0
15
votes
16
replies
2.2k
views
ncbi error report log for validate fastq issue
sra-tools
updated 13 months ago by 146k • written 13 months ago by ★ 1.2k
15
votes
21
replies
1.6k
views
Expression analysis of LncRNA from RNA-seq data
expression lncrna
8 months ago by analyst ▴ 50
15
votes
11
replies
8.0k
views
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
RNA-Seq QC
6.0 years ago by jackgrayner ▴ 100
15
votes
14
replies
2.1k
views
how can interpret these biologically weird results?
RNA-Seq
updated 3.8 years ago by 20 • written 7.0 years ago by ▴ 330
14
votes
8
replies
5.1k
views
Unable To Replicate Splice Junction In Tophat
tophat2 bam
11.1 years ago by Dan D 7.4k
14
votes
30
replies
3.9k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq rna-seq alignment next-gen
5.5 years ago by Malka ▴ 90
14
votes
20
replies
3.5k
views
6 follow
Clustering in single cell
seurat single-cell
7 days ago by Chris ▴ 340
14
votes
18
replies
5.3k
views
GATK Haplotype Caller
next-gen GATK haplotype caller contigs
updated 7.8 years ago by 20 • written 8.0 years ago by ▴ 50
14
votes
10
replies
1.6k
views
How to remove center population from seurat cluster
single-cell
10 months ago by synat.keam ▴ 100
14
votes
5
replies
3.3k
views
bioinformatics basic training
genome
updated 19 months ago by 44k • written 9.9 years ago by • 0
14
votes
16
replies
2.2k
views
Why are some mapped reads not mapped completely?
RNA-Seq mapping
updated 4.0 years ago by 15k • written 4.0 years ago by ▴ 80
13
votes
7
replies
6.9k
views
Why some probes have "NA" for gene symbol and Entrez ID?
affymetrix microarray NA genesymbol
updated 7.9 years ago by 20 • written 8.0 years ago by ▴ 260
13
votes
19
replies
5.7k
views
bbmerge not joining paired-end reads
bbmerge alignment
6.9 years ago by bioplanet ▴ 60
13
votes
13
replies
9.5k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R SNP
updated 6.7 years ago by 104k • written 6.7 years ago by ▴ 70
13
votes
16
replies
7.8k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa samtools mpileup
5.8 years ago by DNAngel ▴ 250
13
votes
13
replies
1.7k
views
Is reproducibility of identified variants in a gene important in Sanger sequencing?
reproducibility sanger sequencing variants
5.0 years ago by DanielC ▴ 170
13
votes
16
replies
6.5k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon mask trimming fastq
7.8 years ago by Paul ★ 1.5k
13
votes
6
replies
4.3k
views
bcftools isec -n operators
bcftools intersect
updated 3.2 years ago by 44k • written 4.8 years ago by ▴ 200
13
votes
13
replies
19k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq FastQC QC GC-content
5.2 years ago by Arindam Ghosh ▴ 530
13
votes
24
replies
5.2k
views
Error of bam-to-sam conversion using samtools
samtools TopHat2 RNA-Seq BAM SAM
updated 7.6 years ago by 146k • written 7.6 years ago by ▴ 480
13
votes
4
replies
23k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage depth read depth
7.5 years ago by ariel.balter ▴ 260
12
votes
21
replies
3.6k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP prs gwas PRSice Plink
updated 5.2 years ago by 20 • written 5.3 years ago by ▴ 30
1,000 results • Page 1 of 20
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Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by ATpoint 85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type by conmul • 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
Comment: How to determine whether it is 10x data by king • 0
Thank you for your answer, it's very inspiring.
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Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
Comment: Can a read be aligned more than once? by GenoMax 146k
Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
Comment: Statistical test to be used for dataset by allingt • 0
The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
Comment: dittoHeatmap; adding column labels on the heatmap by jared.andrews07 ★ 18k
I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
Comment: Comparing GSEA mutant data to wild type by allingt • 0
What do you mean by "significant gene"? How did you perform GSEA and on how did you rank your genes for it? From guesswork I might initiall…
Comment: Genes of Interest in a Multi-Tissue Analysis by allingt • 0
The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
Comment: WGCNA: Why are my brown, yellow, and other modules not visible in the gene dendr by allingt • 0
Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
Comment: Why does WGCNA use weighted correlation instead of Pearson correlation? by allingt • 0
The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
Comment: dittoHeatmap; adding column labels on the heatmap by Varun Gupta ★ 1.3k
any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
Comment: How can I determine the p-value of genes within each identified module in WGCNA? by allingt • 0
What p-value do you mean? When and how did you calculate it?
Answer: What is a genomic range that would almost always get decent WGS coverage but is by i.sudbery 20k
What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
Answer: Using NumReads column of quants.genes.sf file to build DESeq2 input by i.sudbery 20k
One of the improvements that the using the `salmon` -> `tximport` -> `DESeq2` pipeline, over just a `counts`->`DESeq2` pipeline is the abil…
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