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Tutorial: A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics computational-biology
updated 5 months ago by 40k • written 7.5 years ago by ★ 3.2k
13
votes
3
replies
11k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 5 weeks ago by ▴ 20 • written 6.5 years ago by ★ 1.6k
2
votes
3
replies
2.5k
views
Tutorial: It's about the journey, and not the destination
R network
updated 4 months ago by 40k • written 6.5 years ago by ★ 1.2k
1
vote
3
replies
3.0k
views
Tutorial: resolving error of sspace_standard
software-error Assembly
updated 5 months ago by 40k • written 7.1 years ago by ▴ 300
0
votes
3
replies
2.4k
views
Tutorial: Automatic Primer Design
Assembly sequence
updated 13 months ago by 40k • written 7.9 years ago by ▴ 40
72
votes
3
replies
36k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 22 months ago by 40k • written 9.2 years ago by 98k
6
votes
3
replies
4.3k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 6 months ago by 40k • written 4.9 years ago by ▴ 40
15
votes
3
replies
4.4k
views
Tutorial: NCBI blast tutorial
ncbi blast
updated 5 months ago by 40k • written 7.4 years ago by 11k
11
votes
3
replies
1.3k
views
Tutorial: Creating great documentation for bioinformatics software
Software-Documentation
updated 5 months ago by 40k • written 7.2 years ago by 7.1k
4
votes
3
replies
4.3k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 6 months ago by 40k • written 5.5 years ago by ★ 3.9k
1
vote
3
replies
687
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
5 months ago by barslmn ★ 1.8k
8
votes
3
replies
2.6k
views
Tutorial: Free online interactive Ensembl training
ensembl training genome
updated 14 months ago by 40k • written 7.6 years ago by 23k
10
votes
3
replies
4.3k
views
Tutorial: Video: Alternative Splicing and Primer Design
RNA-Seq IGB
updated 8 months ago by 40k • written 9.0 years ago by ▴ 860
3
votes
3
replies
8.3k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 4 months ago by 40k • written 5.8 years ago by ▴ 100
0
votes
3
replies
50k
views
Tutorial: Installation VMD on LINUX_64
gromacs VMD
updated 5 months ago by 40k • written 7.3 years ago by ▴ 10
18
votes
2
replies
5.7k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 4 months ago by 40k • written 6.4 years ago by 5.2k
1
vote
2
replies
3.1k
views
Tutorial: Standalone BLAST error: UnexpectedTagClassByte
software-error blast
updated 11 months ago by 40k • written 8.2 years ago by ▴ 10
2
votes
2
replies
8.2k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 4 months ago by 40k • written 5.8 years ago by ★ 2.4k
15
votes
2
replies
2.8k
views
Tutorial: Introduction to bedtools.
bedtools
updated 6 months ago by 40k • written 8.9 years ago by 12k
2
votes
2
replies
1.8k
views
Tutorial: Human mitochondrial DNA annotation in SnpEff
chrMT SNP snpEff
updated 6 months ago by 40k • written 3.2 years ago by 3.2k
0
votes
2
replies
5.2k
views
Tutorial: Install AMOS on Ubuntu 13.10
sequencing alignment software-error next-gen
updated 23 months ago by 40k • written 9.2 years ago by 9.7k
22
votes
2
replies
5.8k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 5 months ago by 40k • written 6.9 years ago by ★ 2.1k
85
votes
2
replies
56k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 6 months ago by 40k • written 10.2 years ago by 11k
4
votes
2
replies
439
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 5 weeks ago by 40k • written 5 weeks ago by ★ 2.3k
4
votes
2
replies
3.4k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
NGS sequencing Julia OpenGene
updated 6 months ago by 40k • written 7.6 years ago by ★ 2.4k
0
votes
2
replies
2.5k
views
Tutorial: Webinar on 'An integrated RNA and DNA approach to unravel genetic regulation in cancer' on 25 Feb
SNP cancer gene-regulation multiomics rna-seq
updated 17 months ago by 40k • written 8.6 years ago by ▴ 70
15
votes
2
replies
6.6k
views
Tutorial: Genotype And Snp Calling Review Papers
snp
updated 7 months ago by 40k • written 11.1 years ago by 98k
3
votes
2
replies
5.1k
views
Tutorial: Reorder Vcf Files
vcf
updated 7 months ago by 40k • written 10.4 years ago by ▴ 60
15
votes
2
replies
1.8k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 11 months ago by ▴ 810 • written 2.0 years ago by ▴ 280
0
votes
2
replies
2.2k
views
Tutorial: COURSE: NGS variant analysis and interpretation for translational research
CNIO course translational
updated 5 months ago by 40k • written 7.1 years ago by ▴ 190
21
votes
2
replies
4.8k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 12 months ago by ▴ 40 • written 2.4 years ago by 8.2k
4
votes
2
replies
2.3k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 20 days ago by 134k • written 3.4 years ago by 76k
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 19 months ago by 40k • written 8.9 years ago by 12k
19
votes
2
replies
3.2k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 4 months ago by 40k • written 6.5 years ago by ▴ 640
3
votes
2
replies
2.4k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 4 months ago by 40k • written 6.4 years ago by ▴ 100
6
votes
2
replies
3.9k
views
Tutorial: GATK method for filtering vcf lines using GT values at all or multisample level.
genome vcf genotype variant-filtration
updated 4 months ago by 40k • written 6.3 years ago by ★ 1.6k
4
votes
2
replies
7.0k
views
Tutorial: Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink gwas
updated 7 months ago by 40k • written 11.4 years ago by 98k
14
votes
2
replies
6.3k
views
Tutorial: ChIP-seq analysis tutorial
ChIP-Seq
updated 5 months ago by 40k • written 8.1 years ago by ★ 3.4k
7
votes
2
replies
11k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 14 months ago by 40k • written 7.6 years ago by ★ 1.8k
18
votes
2
replies
9.7k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 18 months ago by 40k • written 8.9 years ago by ▴ 860
3
votes
2
replies
2.1k
views
Tutorial: Running fastq_screen on your data
fastqscreen
18 months ago by rohitsatyam102 ▴ 750
6
votes
2
replies
2.5k
views
Tutorial: Tutorial Bioinformatics Static Website
website
updated 6 months ago by 40k • written 9.7 years ago by ▴ 610
42
votes
2
replies
17k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
7
votes
2
replies
3.4k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 7 months ago by 40k • written 11.0 years ago by 11k
60
votes
2
replies
7.1k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
7
votes
2
replies
1.8k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 4 months ago by 40k • written 6.1 years ago by ▴ 90
3
votes
2
replies
3.6k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 4 months ago by 40k • written 6.5 years ago by ▴ 30
6
votes
2
replies
1.4k
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
2.1 years ago by Kevin Blighe 86k
7
votes
2
replies
1.6k
views
Tutorial: A tale of two heatmap function
clustering heatmap
updated 5 months ago by 40k • written 7.0 years ago by ★ 3.4k
5
votes
2
replies
2.1k
views
Tutorial: Using Bedtools Closest (closestBed) to make distance histograms of protein binding frequency near all types of pre-RNA junctions (e.g. exon-intron an…
preRNA closestBed bedtools-closest bedtools
updated 6 months ago by 40k • written 4.7 years ago by ▴ 10
379 results • Page 4 of 8
Recent Votes
Comment: Low Alignment rate
Answer: Filter transcription factors
Answer: Filter transcription factors
Answer: Filter transcription factors
Comment: Integrated Seurat object change name of the two conditions
Comment: Integrated Seurat object change name of the two conditions
Concatenating fastq.gz files across lanes
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Popular Question to adeizadavid ▴ 10
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Recent Replies
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool? by ATpoint 76k
Never tried, so idk. Why wouldn't it support it?
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool? by ATpoint 76k
I never tried conda images but since `mamba > conda` I guess mambaforge is better.
Comment: Filter human transcription factors by Chris ▴ 180
Thank you so much!
Comment: Filter human transcription factors by Chris ▴ 180
Yes, I do GO and GSEA to get pathway. I download the background gene at https://www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp#C3 Th…
Answer: Visualize where kmers are on a reference genome by Alex Reynolds 35k
Make a bigBed file: https://www.biostars.org/p/9546293/ Then view it on the UCSC Genome Browser: http://genome.ucsc.edu/goldenPath/help/…
Comment: Integrated Seurat object change name of the two conditions by camillab. ▴ 130
great! thank you very much!
Answer: Filter transcription factors by jared.andrews07 ★ 15k
[This database](http://humantfs.ccbr.utoronto.ca/download.php) has been the best I've found.
Comment: Filter transcription factors by Ram 40k
What have you tried? Have you looked at GO annotations?
Comment: how to identify uniq genes between two gff files. by nikhil ▴ 10
yes @juke34 , I tried agat_sp_compare_two_annotations.pl for both gff files and got comparative output in table format. Thank you very muc…
Comment: Integrated Seurat object change name of the two conditions by Amitm ★ 2.2k
Yes, its similar structure. This snippet should add a new metadata column "sample.New" with what you want to do # Assuming a seurat obj. c…
Comment: Low Alignment rate by biofalconch ▴ 970
Yeap, you can sample your reads with `seqtk` like this: seqtk sample -s100 read2.fq 100 > Sample.fq Take a couple and run them throug…
Answer: obtaining circular RNAs' sequences from circBase by Barry Digby ★ 1.2k
You won't find them on circBase. circAtlas has the mature spliced sequence available. You can [search for circRNAs](https://ngdc.cncb.a…
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool? by Ram 40k
\#TIL mambaforge - better than continuum's conda images I'm guessing?
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool? by arriyaz.nstu ▴ 30
If the laptop doesn't support WSL2, then will the Docker (with linux) work?
Comment: Integrated Seurat object change name of the two conditions by camillab. ▴ 130
thanks but my metadata looks different from yours. Will it work even there are not the same "structure"? or…
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