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41
votes
55
replies
11k
views
6 follow
hash function for DNA sequences
hash hashing DNA
7.7 years ago by midox ▴ 290
27
votes
17
replies
20k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
24 months ago by Leite ★ 1.3k
24
votes
25
replies
7.4k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq beta diversity metagenomics
3.3 years ago by dpc ▴ 240
23
votes
22
replies
45k
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 12 months ago by • 0 • written 5.6 years ago by ▴ 250
23
votes
10
replies
5.5k
views
How to predict individual ethnicity information by using hapmap data
SNP Ethnicity Hapmap
updated 2.6 years ago by 86k • written 5.8 years ago by ▴ 40
22
votes
20
replies
2.3k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast RNA-Seq genome gene
updated 7 months ago by 41k • written 7.4 years ago by ★ 3.4k
22
votes
19
replies
2.9k
views
targets of a list of miRNAs
miRNAs RNA-Seq DEanalysis target-prediction
7.2 years ago by fi1d18 ★ 4.2k
20
votes
17
replies
5.7k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein filtering bbmap bbduk phix
6.3 years ago by Anand Rao ▴ 600
20
votes
17
replies
2.7k
views
How to add "transcript" feature to a gtf file?
gtf
updated 4 months ago by ★ 1.1k • written 2.8 years ago by ▴ 110
20
votes
15
replies
28k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 16 months ago by 41k • written 7.9 years ago by ▴ 200
19
votes
43
replies
5.0k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.3 years ago by nazaninhoseinkhan ▴ 510
18
votes
7
replies
1.2k
views
How to calculate if statistically a variable of a bulk RNA-seq affects the comparison of interest?
DESeq2 Variable RNA-seq
14 months ago by Rafael Soler ★ 1.2k
18
votes
4
replies
8.5k
views
How To Find Rna-Seq Data Of Published Papers?
geo next-gen RNA-seq
updated 9 months ago by 41k • written 10.3 years ago by ▴ 940
18
votes
19
replies
2.0k
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 12 months ago by 41k • written 4.9 years ago by • 0
17
votes
8
replies
2.2k
views
Number of unique authors in PubMed in last 10 years
PubMed
7.7 years ago by nejc ▴ 50
17
votes
19
replies
2.5k
views
Sorting sequences according header
software error sequence Assembly next-gen
7.3 years ago by Gian77 ▴ 60
17
votes
13
replies
6.2k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment genome sequencing
6.5 years ago by lghust2011 ▴ 110
17
votes
37
replies
4.2k
views
No alias or index file found for protein database
next-gen software error sequence
updated 4.5 years ago by 20 • written 4.6 years ago by ▴ 500
16
votes
14
replies
16k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters trimmomatic RNA-seq
5.4 years ago by salamandra ▴ 550
16
votes
38
replies
16k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 19 months ago by 41k • written 8.8 years ago by ▴ 920
16
votes
16
replies
2.9k
views
Using DESeq2 results for building a classifier
deseq2 RNA-Seq differentially expressed genes
5.7 years ago by bioinfo456 ▴ 150
16
votes
18
replies
5.0k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 4.3 years ago by ★ 25k • written 4.3 years ago by • 0
16
votes
10
replies
5.3k
views
6 follow
Powerful desktop computer for genomics
next-gen sequencing ChIP-Seq RNA-Seq
7.5 years ago by Alternative ▴ 270
16
votes
21
replies
1.9k
views
Why there are different hit for a same gene in different species
gene blast ortholog paralog
7.2 years ago by Farbod ★ 3.4k
16
votes
17
replies
3.0k
views
6 follow
RNA seq pipeline
RNA-Seq
6.1 years ago by dimitrischat ▴ 210
15
votes
14
replies
2.9k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq bwa mem bowtie2 alignment
5.9 years ago by John ▴ 270
15
votes
16
replies
1.3k
views
ncbi error report log for validate fastq issue
sra-tools
updated 9 weeks ago by 136k • written 9 weeks ago by ★ 1.1k
15
votes
6
replies
11k
views
6 follow
MAF vs VAF
sequencing
5.7 years ago by lauren.wahyudi ▴ 50
15
votes
19
replies
1.7k
views
trimmomaric command for a fasta file?
trimmomatic
updated 5.6 years ago by 41k • written 5.6 years ago by • 0
15
votes
14
replies
1.7k
views
how can interpret these biologically weird results?
RNA-Seq
updated 2.9 years ago by 20 • written 6.1 years ago by ▴ 330
14
votes
8
replies
4.8k
views
Unable To Replicate Splice Junction In Tophat
tophat2 bam
10.1 years ago by Dan D 7.4k
14
votes
18
replies
4.6k
views
GATK Haplotype Caller
next-gen GATK haplotype caller contigs
updated 6.9 years ago by 20 • written 7.1 years ago by ▴ 50
14
votes
30
replies
3.1k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq rna-seq alignment next-gen
4.6 years ago by Malka ▴ 80
14
votes
16
replies
1.7k
views
Why are some mapped reads not mapped completely?
RNA-Seq mapping
updated 3.1 years ago by 14k • written 3.1 years ago by ▴ 80
14
votes
5
replies
3.0k
views
bioinformatics basic training
genome
updated 8 months ago by 41k • written 9.0 years ago by • 0
14
votes
18
replies
1.4k
views
Clustering in single cell
seurat single-cell
updated 6 weeks ago by ▴ 170 • written 9 weeks ago by ▴ 230
13
votes
7
replies
6.3k
views
Why some probes have "NA" for gene symbol and Entrez ID?
affymetrix microarray NA genesymbol
updated 7.0 years ago by 20 • written 7.0 years ago by ▴ 260
13
votes
24
replies
4.1k
views
Error of bam-to-sam conversion using samtools
samtools TopHat2 RNA-Seq BAM SAM
updated 6.7 years ago by 136k • written 6.7 years ago by ▴ 480
13
votes
16
replies
5.6k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon mask trimming fastq
6.9 years ago by Paul ★ 1.5k
13
votes
22
replies
10k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch effects
updated 6.2 years ago by 20 • written 6.4 years ago by ★ 1.3k
13
votes
16
replies
6.7k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa samtools mpileup
4.9 years ago by DNAngel ▴ 240
13
votes
13
replies
1.3k
views
Is reproducibility of identified variants in a gene important in Sanger sequencing?
reproducibility sanger sequencing variants
4.1 years ago by DanielC ▴ 160
13
votes
19
replies
5.0k
views
bbmerge not joining paired-end reads
bbmerge alignment
6.0 years ago by bioplanet ▴ 60
13
votes
13
replies
16k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq FastQC QC GC-content
4.3 years ago by Arindam Ghosh ▴ 510
13
votes
11
replies
6.6k
views
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
RNA-Seq QC
5.1 years ago by jackgrayner ▴ 80
13
votes
13
replies
8.6k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R SNP
updated 5.7 years ago by 104k • written 5.7 years ago by ▴ 70
12
votes
11
replies
3.1k
views
How To Get Snp Genotypes
snp genotyping
updated 12.3 years ago by 11k • written 12.6 years ago by ▴ 20
12
votes
10
replies
2.7k
views
7 follow
SAM / BAM alignments
SAM BAM
6.9 years ago by John 13k
12
votes
17
replies
4.4k
views
How do I generate all possible Newick Tree permutations for a set of species given an outgroup in Python?
Python Newick phylogenetics tree phylogeny
6.1 years ago by anonymous1192976466 ▴ 50
12
votes
8
replies
3.0k
views
How to change depth of sequence in RNA-seq fastq files
depth of sequence RNA-Seq
6.9 years ago by statfa ▴ 740
1,000 results • Page 1 of 20
Recent Votes
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: GO categorization
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
Answer: Problematic fastq files...How can we trust them?
Comment: Problematic fastq files...How can we trust them?
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Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Brian Bushnell 19k
It's not a silly question! And yes, it can be done. JGI is currently testing various binning tools to try to find the best protocol for t…
Answer: GO categorization by geneontologyhelp ▴ 270
[We have this in our FAQ][1]. PANTHER version 18.0, which powers the enrichment analysis on our homepage, has [143 species][2] loaded and …
Comment: Problematic fastq files...How can we trust them? by blackadder ▴ 30
Thanks for the feedback fellas! I agree with the aforementioned!
Comment: Which program, tool, or strategy do you use to visualize genomic rearrangements? by cmdcolin ★ 3.4k
i collect a large list of tools for visualization, some are specialized for SVs and re-arrangements. you can filter by tag (SV, CNV, compar…
Answer: The number of variations in the pan-genome is reduced compared to the variations by Jordan M Eizenga ▴ 410
If variants overlap in the genome, `vg deconstruct` will combine them into one locus with multiple alleles. If your input VCF has a lot of …
Answer: How to find node Postion and source(sample) ? by Jordan M Eizenga ▴ 410
You can use `vg find -P` for this. This command is not really designed to be used frequently throughout the genome (each invocation loads t…
Comment: How Can I move the scattered dots more closer into the center of box ? by Brian Bushnell 19k
I would just draw them in by hand where you want them.
Comment: How to identify CG, CHG, or CHH from MeDIP data by Tm ★ 1.1k
I know that CpG types can be identified using whole genome bisulphite data. But could it be possible using MeDIP data too? We tried using Q…
Comment: Problematic fastq files...How can we trust them? by Brian Bushnell 19k
I'd have to agree there... while you can generally recover a fastq to the point that it is spec-compliant, you don't know how or why the f…
Answer: Finding human .vcf files online to download by cmdcolin ★ 3.4k
---------- some common ones include 1000 genomes vcf (large, multi-sample) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ …
Comment: GO categorization by m.habib • 0
Thanks Istvan for your reply. I think these programs will do the same as Trinotate. Trinotate searches against numerous databases and gener…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by jv ★ 1.2k
I wonder if using cell hashing, which would allow pooling of cells from multiple samples before droplet formation, could improve things her…
Comment: Where Can I Find The Basepair Positions Of Chromosome Bands? by Malachi Griffith 19k
And the hg38 version can be found here: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz And for convenience, upda…
Answer: How Can I move the scattered dots more closer into the center of box ? by Trivas ★ 1.5k
You added a position dodge on your boxplot but not on your points.
Comment: How Can I move the scattered dots more closer into the center of box ? by ATpoint 78k
Please understand that biostars is not a helpdesk for trivial ggplot questions. Google it and find help on previous StackExchange sites, or…
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