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1,000 results • Page 1 of 20
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41
votes
55
replies
9.8k
views
6 follow
hash function for DNA sequences
hash hashing DNA
7.0 years ago by midox ▴ 290
27
votes
17
replies
17k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
15 months ago by Leite ★ 1.2k
24
votes
25
replies
5.7k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq beta diversity metagenomics
2.7 years ago by dpc ▴ 240
23
votes
22
replies
38k
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 4 months ago by • 0 • written 4.9 years ago by ▴ 250
23
votes
10
replies
5.0k
views
How to predict individual ethnicity information by using hapmap data
SNP Ethnicity Hapmap
updated 23 months ago by 85k • written 5.1 years ago by ▴ 40
22
votes
20
replies
2.0k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
RNA-Seq blast gene genome Forum
6.7 years ago by Farbod ★ 3.4k
22
votes
19
replies
2.4k
views
targets of a list of miRNAs
miRNAs RNA-Seq DEanalysis target-prediction
6.5 years ago by fi1d18 ★ 4.1k
20
votes
15
replies
25k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 8 months ago by 38k • written 7.2 years ago by ▴ 190
19
votes
43
replies
4.0k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.6 years ago by nazaninhoseinkhan ▴ 500
18
votes
19
replies
1.6k
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 4 months ago by 38k • written 4.2 years ago by • 0
18
votes
7
replies
814
views
How to calculate if statistically a variable of a bulk RNA-seq affects the comparison of interest?
DESeq2 Variable RNA-seq
6 months ago by Rafael Soler ★ 1.1k
18
votes
4
replies
8.1k
views
How To Find Rna-Seq Data Of Published Papers?
geo next-gen RNA-seq
updated 4 weeks ago by 38k • written 9.7 years ago by ▴ 930
17
votes
37
replies
3.3k
views
No alias or index file found for protein database
next-gen software error sequence
updated 3.8 years ago by 20 • written 4.0 years ago by ▴ 470
17
votes
13
replies
5.4k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment genome sequencing
5.9 years ago by lghust2011 ▴ 100
17
votes
19
replies
2.1k
views
Sorting sequences according header
software error sequence Assembly next-gen
6.6 years ago by Gian77 ▴ 60
17
votes
8
replies
1.9k
views
Number of unique authors in PubMed in last 10 years
PubMed
7.0 years ago by nejc ▴ 50
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 11 months ago by 38k • written 8.1 years ago by ▴ 920
16
votes
10
replies
4.7k
views
6 follow
Powerful desktop computer for genomics
next-gen sequencing ChIP-Seq RNA-Seq
6.9 years ago by Alternative ▴ 270
16
votes
17
replies
2.7k
views
6 follow
RNA seq pipeline
RNA-Seq
5.4 years ago by dimitrischat ▴ 180
16
votes
14
replies
14k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters trimmomatic RNA-seq
4.8 years ago by salamandra ▴ 530
16
votes
21
replies
1.6k
views
Why there are different hit for a same gene in different species
gene blast ortholog paralog
6.5 years ago by Farbod ★ 3.4k
16
votes
16
replies
2.4k
views
Using DESeq2 results for building a classifier
deseq2 RNA-Seq differentially expressed genes
5.0 years ago by bioinfo456 ▴ 150
16
votes
8
replies
1.6k
views
8 follow
What are the most important unresolved problems in Bioinformatics?
problem unresolved bioinformatics
updated 6.4 years ago by 20 • written 6.5 years ago by ★ 2.4k
16
votes
18
replies
3.8k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 3.6 years ago by ★ 23k • written 3.6 years ago by • 0
15
votes
14
replies
2.3k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq bwa mem bowtie2 alignment
5.2 years ago by John ▴ 270
15
votes
14
replies
1.4k
views
how can interpret these biologically weird results?
RNA-Seq
updated 2.2 years ago by 20 • written 5.4 years ago by ▴ 330
15
votes
19
replies
1.3k
views
trimmomaric command for a fasta file?
trimmomatic
updated 4.9 years ago by 38k • written 4.9 years ago by • 0
14
votes
17
replies
4.9k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein filtering bbmap bbduk phix
5.6 years ago by Anand Rao ▴ 550
14
votes
8
replies
4.6k
views
Unable To Replicate Splice Junction In Tophat
tophat2 bam
9.5 years ago by Dan D 7.4k
14
votes
5
replies
2.7k
views
bioinformatics basic training
genome
updated 18 days ago by 38k • written 8.3 years ago by • 0
14
votes
16
replies
1.3k
views
Why are some mapped reads not mapped completely?
RNA-Seq mapping
updated 2.4 years ago by 14k • written 2.4 years ago by ▴ 80
14
votes
18
replies
4.1k
views
GATK Haplotype Caller
next-gen GATK haplotype caller contigs
updated 6.2 years ago by 20 • written 6.4 years ago by ▴ 50
14
votes
30
replies
2.5k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq rna-seq alignment next-gen
3.9 years ago by Malka ▴ 70
13
votes
7
replies
5.8k
views
Why some probes have "NA" for gene symbol and Entrez ID?
affymetrix microarray NA genesymbol
updated 6.3 years ago by 20 • written 6.4 years ago by ▴ 250
13
votes
24
replies
3.3k
views
Error of bam-to-sam conversion using samtools
samtools TopHat2 RNA-Seq BAM SAM
updated 6.1 years ago by 127k • written 6.1 years ago by ▴ 480
13
votes
6
replies
9.9k
views
6 follow
MAF vs VAF
sequencing
5.0 years ago by lauren.wahyudi ▴ 40
13
votes
13
replies
7.8k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R SNP
updated 5.1 years ago by 103k • written 5.1 years ago by ▴ 70
13
votes
16
replies
5.4k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa samtools mpileup
4.2 years ago by DNAngel ▴ 240
13
votes
22
replies
8.9k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch effects
updated 5.5 years ago by 20 • written 5.7 years ago by ★ 1.3k
13
votes
19
replies
4.3k
views
bbmerge not joining paired-end reads
bbmerge alignment
5.3 years ago by bioplanet ▴ 60
13
votes
13
replies
982
views
Is reproducibility of identified variants in a gene important in Sanger sequencing?
reproducibility sanger sequencing variants
3.4 years ago by DanielC ▴ 160
13
votes
16
replies
5.0k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon mask trimming fastq
6.2 years ago by Paul ★ 1.5k
12
votes
12
replies
4.4k
views
Need A Script That Finds Whether A String In One Column Matches In Other Columns Of The Same Row
perl
updated 9.3 years ago by 97k • written 9.3 years ago by ★ 1.4k
12
votes
28
replies
1.8k
views
Calculating the expression level of genes
Gene expression RNA-Seq R
4.8 years ago by Za ▴ 140
12
votes
10
replies
3.6k
views
Speed up BLASTp vs NCBI nr database
blast
6.8 years ago by biotech ▴ 560
12
votes
10
replies
2.3k
views
7 follow
SAM / BAM alignments
SAM BAM
6.2 years ago by John 13k
12
votes
11
replies
2.8k
views
How To Get Snp Genotypes
snp genotyping
updated 11.6 years ago by 11k • written 12.0 years ago by ▴ 20
12
votes
8
replies
608
views
Align 16S sequence to a reference
16S sequence alignment
updated 6 months ago by 3.4k • written 6 months ago by ▴ 120
12
votes
13
replies
2.1k
views
Gene Expression and Systems Biology (homework)
gene homework
updated 3 months ago by 38k • written 7.7 years ago by • 0
12
votes
8
replies
2.6k
views
How to change depth of sequence in RNA-seq fastq files
depth of sequence RNA-Seq
6.2 years ago by statfa ▴ 700
1,000 results • Page 1 of 20
Recent Votes
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor
SSPACE for scaffolding
Answer: Snakemake workflow for trimmomatic
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
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Recent Replies
Comment: SKAT in R by Eliza ▴ 20
@acvill can you sujjest maybe pther tools , methods for this ? ( also for every SNP i have data how many patients had the hetro/homozygous…
Comment: TCGA-BRCA tissue and RNAseq problem by pinheirofabiano ▴ 10
Go to https://portal.gdc.cancer.gov > Exploration > select TCGA and the cancer type you want > select case ID to download the files and hav…
Answer: Snakemake workflow for trimmomatic by antoine.fauchois92 • 0
Thank you very much for your reply ! It's working now !
Comment: Dependent p values by Eliza ▴ 20
@lchart I'm sorry for asking another of questions but I'm new to this field , can you please explain a little more how to use SKAT , saige…
Comment: How to deal with the probe id mapping to multiple gene ids? by dare_devil ★ 1.7k
similar question [here][1], [here][2] and [here][3] [1]: https://support.bioconductor.org/p/54838/ [2]: https://support.bioconductor.…
Comment: How to deal with the probe id mapping to multiple gene ids? by dare_devil ★ 1.7k
@genomax I have used the same platform file only. If you look at probe id and their corresponding `Gene Symbol` or `ENTREZ_GENE_ID` you can…
Comment: How to deal with the probe id mapping to multiple gene ids? by GenoMax 127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned. [1]: https://www.ncbi.nlm.nih.go…
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL by rpolicastro 11k
`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
Comment: Snakemake doesn't recognize output files even though they are created by DdogBoss • 0
Yes, it completed the dry run. What other information do you need?
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Based on my personal thought, I think the se from LDSC output probably needs to be transferred using Delta method based on Fisher transform…
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Hi, Are you able to find an answer for this? I have the exact question! YL
Answer: Gene duplicate by ATpoint 71k
Use use ensembID_geneName as gene identifier to avoid that. These duplicate names exist as genes so removing them is somewhat not really da…
Comment: Gene duplicate by Ram 38k
> some Ensembl IDs that are the same Please show us some examples.
Comment: R package for functional enrichment and depletion analysis by rpolicastro 11k
What you're describing is a simulation of the hypergeometric test, so if you want an exact solution you could use the function `fora` from …
Comment: How to remove duplicate reads after ONT basecalling from fastq.gz files by Darrenjdd • 0
Perfect! Thank you!
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