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383 results • Page 3 of 8
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3
votes
3
replies
8.4k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 6 months ago by 41k • written 5.9 years ago by ▴ 100
18
votes
22
replies
8.4k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 10 weeks ago by ▴ 20 • written 4.0 years ago by 8.4k
81
votes
8
replies
8.3k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 9 months ago by 41k • written 9.5 years ago by 19k
14
votes
0
replies
8.2k
views
Tutorial: Video: ChIP-Seq Analysis and Visualization using Galaxy and IGB.
IGB ChIP-Seq Galaxy MACS RNA-Seq
updated 20 months ago by 41k • written 8.9 years ago by ▴ 860
8
votes
7
replies
8.1k
views
Tutorial: Getting Cegma/Genewise To Work On Centos, Rhel
centos genewise rhel cegma
updated 22 months ago by 41k • written 10.0 years ago by ★ 2.6k
12
votes
5
replies
8.1k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 7 months ago by 41k • written 7.5 years ago by ★ 9.3k
19
votes
13
replies
7.9k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 29 days ago by • 0 • written 17 months ago by 78k
0
votes
0
replies
7.9k
views
Tutorial: Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R eviews
updated 6 months ago by 41k • written 5.9 years ago by ▴ 10
50
votes
1
reply
7.9k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 9 months ago by 41k • written 3.2 years ago by 78k
16
votes
11
replies
7.9k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
8 months ago by Ram 41k
20
votes
2
replies
7.7k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 6 months ago by 41k • written 6.0 years ago by ★ 3.4k
6
votes
1
reply
7.7k
views
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat RNA-seq cufflinks
updated 9 months ago by 41k • written 11.6 years ago by 99k
12
votes
0
replies
7.6k
views
Tutorial: Plot average methylation levels across TSS region
bedtools RRBS R methylation
updated 20 months ago by 41k • written 8.8 years ago by ★ 4.7k
42
votes
19
replies
7.6k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 9 months ago by 41k • written 10.8 years ago by 4.1k
26
votes
17
replies
7.3k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 14 months ago by 41k • written 9.3 years ago by 6.0k
32
votes
4
replies
7.3k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 8 months ago by 41k • written 5.1 years ago by ★ 1.6k
6
votes
4
replies
7.3k
views
Tutorial: Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization ChIP-seq RNA-seq ucsc-genome-browser bigwig
updated 9 months ago by 41k • written 10.7 years ago by 11k
60
votes
2
replies
7.2k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 9 months ago by 41k • written 11.3 years ago by 99k
24
votes
4
replies
7.1k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 8 months ago by 41k • written 4.3 years ago by 78k
12
votes
11
replies
7.1k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI Bioproject SRA BioSample
updated 6 months ago by 41k • written 6.7 years ago by ★ 2.4k
4
votes
2
replies
7.1k
views
Tutorial: Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink gwas
updated 9 months ago by 41k • written 11.5 years ago by 99k
64
votes
5
replies
7.1k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 13 months ago by 41k • written 8.3 years ago by 12k
15
votes
1
reply
6.8k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl SAM blast BED
updated 6 months ago by 41k • written 6.0 years ago by ★ 3.0k
15
votes
2
replies
6.7k
views
Tutorial: Genotype And Snp Calling Review Papers
snp
updated 9 months ago by 41k • written 11.3 years ago by 99k
2
votes
0
replies
6.7k
views
Tutorial: How to - Install Python packages in a virtual environment (virtualenv)
ubuntu cutadapt virtualenv python windows
updated 6 months ago by 41k • written 6.0 years ago by ▴ 320
5
votes
5
replies
6.7k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 6 months ago by 41k • written 6.1 years ago by ▴ 130
21
votes
5
replies
6.6k
views
Tutorial: Analysis of single-cell RNA-seq data
single-cell RNA-Seq
updated 7 months ago by 41k • written 7.4 years ago by ★ 1.5k
16
votes
0
replies
6.5k
views
Tutorial: Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
course training
updated 9 months ago by 41k • written 11.4 years ago by 99k
8
votes
12
replies
6.5k
views
Tutorial: Create your own VPN to access work resources from home
tinyproxy OpenVPN VPN
updated 7 months ago by 41k • written 7.5 years ago by 13k
8
votes
2
replies
6.4k
views
Tutorial: Troubleshooting issues with SURPI pipeline for pathogen identification from complex metagenomic NGS data.
metagenomics clinical-genomics
updated 22 months ago by 41k • written 9.1 years ago by 12k
23
votes
19
replies
6.4k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 7 months ago by 41k • written 7.2 years ago by ★ 2.5k
21
votes
9
replies
6.3k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 9 months ago by 41k • written 10.5 years ago by 9.7k
14
votes
2
replies
6.3k
views
Tutorial: ChIP-seq analysis tutorial
ChIP-Seq
updated 8 months ago by 41k • written 8.2 years ago by ★ 3.6k
21
votes
10
replies
6.3k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 8 months ago by 41k • written 3.2 years ago by 12k
6
votes
0
replies
6.2k
views
Tutorial: Leveraging Flow Order And Flow Signals From Ion Torrent Data
ion-torrent
updated 9 months ago by 41k • written 11.6 years ago by ▴ 360
16
votes
9
replies
6.2k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 17 months ago by ▴ 70 • written 24 months ago by ★ 1.3k
16
votes
6
replies
6.2k
views
Tutorial: How to make your snakefiles self-documenting
snakemake
updated 7 months ago by 41k • written 7.1 years ago by ★ 1.7k
29
votes
5
replies
6.2k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 9 months ago by 41k • written 10.2 years ago by ★ 4.4k
11
votes
0
replies
6.1k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 8 months ago by 41k • written 2.9 years ago by 136k
14
votes
7
replies
6.1k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 8 months ago by 41k • written 7.5 years ago by ★ 3.4k
20
votes
7
replies
6.1k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 8 months ago by 41k • written 5.1 years ago by ▴ 770
14
votes
31
replies
6.1k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 8 months ago by 41k • written 4.3 years ago by 8.4k
18
votes
7
replies
6.0k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 4 months ago by 78k • written 3.7 years ago by 5.7k
4
votes
1
reply
6.0k
views
Tutorial: Chip-Seq Data Analysis Tutorial
chip-seq
updated 9 months ago by 41k • written 11.6 years ago by ▴ 360
34
votes
15
replies
6.0k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 8 months ago by 41k • written 4.5 years ago by ★ 9.3k
36
votes
5
replies
5.9k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 12 weeks ago by ▴ 20 • written 8.4 years ago by ▴ 410
22
votes
2
replies
5.8k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 7 months ago by 41k • written 7.1 years ago by ★ 2.1k
18
votes
2
replies
5.7k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 6 months ago by 41k • written 6.6 years ago by 5.3k
13
votes
6
replies
5.7k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 7 months ago by 41k • written 7.5 years ago by 14k
6
votes
3
replies
5.6k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 9 months ago by 41k • written 11.4 years ago by 99k
383 results • Page 3 of 8
Recent Votes
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?
Comment: Problematic fastq files...How can we trust them?
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Recent Awards • All
Popular Question to beausoleilmo ▴ 560
Commentator to Brian Bushnell 19k
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Recent Replies
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 ▴ 260
[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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