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Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 25 days ago by ▴ 50 • written 3.3 years ago by ▴ 160
7
votes
14
replies
3.2k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 13 months ago by • 0 • written 21 months ago by ▴ 30
51
votes
14
replies
79k
views
10 follow
Tutorial: Using R in Conda
R
updated 8 months ago by 41k • written 3.4 years ago by ▴ 780
75
votes
14
replies
15k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 9 months ago by 41k • written 10.5 years ago by 9.7k
20
votes
14
replies
3.7k
views
Tutorial: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data visualization and exploration (Windows)
ChIP-Seq visualization Windows EaSeq
updated 7 months ago by 41k • written 7.6 years ago by ▴ 460
28
votes
13
replies
12k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 22 months ago by ★ 1.3k • written 2.1 years ago by 99k
17
votes
13
replies
2.0k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 6 months ago by 41k • written 6.7 years ago by 53k
76
votes
13
replies
15k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 2.1 years ago by 41k • written 9.5 years ago by 19k
75
votes
13
replies
66k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 13 months ago by 41k • written 10.0 years ago by ★ 1.2k
64
votes
13
replies
13k
views
11 follow
Tutorial: Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
muTect GATK Picard Exome
updated 21 months ago by 41k • written 9.1 years ago by ★ 2.4k
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
4
votes
13
replies
12k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 5 months ago by 41k • written 4.8 years ago by ▴ 140
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
32
votes
12
replies
29k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 9 months ago by 41k • written 10.1 years ago by 99k
6
votes
11
replies
5.3k
views
6 follow
Tutorial: Add count numbers to headers in a fasta file
genome
updated 9 months ago by 41k • written 7.0 years ago by ▴ 50
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
16
votes
11
replies
14k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
TCGA RNA-seq data-retrieval cBioportal R
updated 8 months ago by 41k • written 7.1 years ago by ★ 4.7k
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
29
votes
10
replies
73k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 8 months ago by 41k • written 2.7 years ago by ★ 1.5k
6
votes
10
replies
5.0k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 8 months ago by 41k • written 5.8 years ago by ▴ 370
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
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
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
65
votes
9
replies
48k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 9 months ago by 41k • written 10.4 years ago by ★ 3.0k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 9 months ago by 41k • written 9.6 years ago by ★ 1.9k
9
votes
9
replies
4.0k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 6 months ago by 41k • written 6.2 years ago by 86k
8
votes
9
replies
11k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq fasta
updated 9 months ago by 41k • written 9.6 years ago by ★ 1.8k
7
votes
8
replies
3.3k
views
Tutorial: Determine if a transcription factor is bound with CENTIPEDE
ChIP-Seq transcription-factor DNase-Seq CENTIPEDE
updated 11 months ago by 41k • written 8.4 years ago by ★ 2.2k
31
votes
8
replies
11k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 9 months ago by 41k • written 9.6 years ago by ▴ 810
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
99
votes
8
replies
28k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 8 months ago by 41k • written 7.8 years ago by ★ 1.1k
39
votes
8
replies
12k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 8 months ago by 41k • written 3.2 years ago by 3.1k
23
votes
8
replies
5.2k
views
Tutorial: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K methylation
updated 23 months ago by 41k • written 9.3 years ago by 24k
13
votes
7
replies
5.6k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 8 months ago by 41k • written 3.2 years ago by 86k
11
votes
7
replies
1.9k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
8 months ago by barslmn ★ 2.0k
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
11
votes
7
replies
14k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk linux bash
updated 6 months ago by 41k • written 6.2 years ago by 86k
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
11
votes
7
replies
9.9k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 6 months ago by 41k • written 2.7 years ago by ▴ 360
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
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
16
votes
7
replies
15k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 8 months ago by 41k • written 4.5 years ago by ▴ 310
49
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 9 months ago by 41k • written 11.3 years ago by 99k
43
votes
6
replies
12k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 9 months ago by 41k • written 9.8 years ago by 6.0k
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
30
votes
6
replies
22k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 14 months ago by 41k • written 11.6 years ago by 99k
44
votes
6
replies
22k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 22 months ago by ▴ 40 • written 2.7 years ago by 12k
11
votes
6
replies
4.8k
views
Tutorial: sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 16 months ago by 41k • written 7.8 years ago by ★ 4.2k
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
31
votes
6
replies
11k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 8 months ago by 41k • written 3.5 years ago by 86k
383 results • Page 2 of 8
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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Popular Question to beausoleilmo ▴ 560
Commentator to Brian Bushnell 19k
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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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