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19
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2
replies
3.3k
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Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 6 months ago by 41k • written 6.7 years ago by ▴ 640
19
votes
13
replies
8.0k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 4 weeks ago by • 0 • written 17 months ago by 78k
19
votes
4
replies
8.7k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 9 months ago by 41k • written 10.8 years ago by 99k
19
votes
3
replies
13k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 16 months ago by 41k • written 7.8 years ago by ★ 9.3k
18
votes
2
replies
5.8k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 6 months ago by 41k • written 6.6 years ago by 5.3k
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
18
votes
2
replies
9.8k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 20 months ago by 41k • written 9.1 years ago by ▴ 860
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 5.8k
18
votes
40
replies
17k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 3.4 years ago by • 0 • written 7.4 years ago by ▴ 170
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
16
votes
5
replies
8.8k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 9 months ago by 41k • written 11.2 years ago by 20k
16
votes
9
replies
6.2k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 18 months ago by ▴ 70 • written 2.0 years 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
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
16
votes
0
replies
13k
views
Tutorial: Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 9 months ago by 41k • written 11.7 years ago by 10k
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
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
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
15
votes
5
replies
12k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 9 months ago by 41k • written 6.0 years ago by ▴ 770
15
votes
1
reply
3.1k
views
Tutorial: Current Topics in Genome Analysis 2016 (collection of educational lectures)
genomics training lectures workshop
updated 8 months ago by 41k • written 7.6 years ago by 19k
15
votes
5
replies
15k
views
Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 8 months ago by 41k • written 7.5 years ago by 20k
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 6.1 years ago by ★ 3.0k
15
votes
3
replies
4.5k
views
Tutorial: NCBI blast tutorial
ncbi blast
updated 8 months ago by 41k • written 7.6 years ago by 11k
15
votes
2
replies
2.9k
views
Tutorial: Introduction to bedtools.
bedtools
updated 9 months ago by 41k • written 9.0 years ago by 12k
15
votes
1
reply
3.5k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 15 months ago by ★ 1.8k • written 23 months ago by 14k
15
votes
2
replies
1.9k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 13 months ago by ▴ 820 • written 2.2 years ago by ▴ 280
15
votes
2
replies
3.6k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 8 months ago by 41k • written 3.2 years ago by 3.1k
15
votes
4
replies
4.4k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 8 months ago by 41k • written 3.4 years ago by ▴ 340
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
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 9 months ago by 41k • written 4.3 years ago by 8.4k
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 7.6 years ago by ★ 3.4k
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
14
votes
2
replies
6.3k
views
Tutorial: ChIP-seq analysis tutorial
ChIP-Seq
updated 8 months ago by 41k • written 8.3 years ago by ★ 3.6k
14
votes
2
replies
2.3k
views
Tutorial: Exploring OpenSNP - an RMarkdown report on crowdsourced genotypes and phenotypes
SNP R
updated 8 months ago by 41k • written 7.7 years ago by 22k
14
votes
0
replies
9.3k
views
Tutorial: How to generate PCA plot and heatmaps in R
heatmap PCA RNA-Seq R
updated 8 months ago by 41k • written 7.2 years ago by ★ 3.6k
13
votes
3
replies
14k
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 3 months ago by ▴ 20 • written 6.7 years ago by ★ 1.6k
13
votes
1
reply
2.7k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 2.5 years ago by ★ 16k • written 2.5 years ago by 86k
13
votes
3
replies
5.0k
views
Tutorial: Video: Visualization of whole genome DNA methylation data in IGB
Bismark BS-Seq RNA-Seq IGB
updated 18 months ago by 41k • written 8.7 years ago by ▴ 860
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
13
votes
6
replies
5.7k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 8 months ago by 41k • written 7.5 years ago by 14k
12
votes
5
replies
2.2k
views
Tutorial: FASTA file split
fasta
updated 8 months ago by 41k • written 3.5 years ago by 8.4k
12
votes
17
replies
2.6k
views
Tutorial: How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola bwa
updated 11 months ago by 41k • written 8.5 years ago by 99k
12
votes
20
replies
13k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 8 months ago by 41k • written 4.5 years ago by ★ 16k
12
votes
0
replies
2.5k
views
Tutorial: Long versus wide data for plotting genomics data in R.
ggplot2 tidyverse data.table R
updated 8 months ago by 41k • written 3.3 years ago by 12k
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
12
votes
4
replies
5.1k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 9 months ago by 41k • written 2.8 years ago by ▴ 130
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
12
votes
4
replies
2.0k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 8 months ago by 41k • written 6.2 years ago by ▴ 590
12
votes
5
replies
8.1k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 8 months ago by 41k • written 7.5 years ago by ★ 9.3k
12
votes
1
reply
4.9k
views
Tutorial: RepSeq data processing and analysis
immunology tcr repseq sequencing repertoire
updated 13 months ago by 41k • written 8.3 years ago by 3.5k
384 results • Page 3 of 8
Recent Votes
Comment: 4 Fastq files for a single run generated by 10X
Comment: 4 Fastq files for a single run generated by 10X
Answer: How do you generate TMM normalized counts using EdgeR?
The Biostar Handbook. A bioinformatics e-book for beginners.
GEO dataset Microarray data analysis help
C: Batch effects : ComBat or removebatcheffects (limma package) ?
Answer: Batch effects : ComBat or removebatcheffects (limma package) ?
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Recent Replies
Comment: How to download multiple genome files using command line (MacOS) using datasets by scholaraspect2008 • 0
by means of that, how should i write my scripting? say i have GCF000001 GCF000002 GCF000003 btw sorry if i wasn't that clear with the …
Comment: DEA Solver Learning Version 8 by GenoMax 136k
Can you add a note about what this software is used for? Content on this site needs to be related to bioinformatics otherwise it may be rem…
Comment: 4 Fastq files for a single run generated by 10X by hkarakurt ▴ 180
Thank you for your detailed answer. I will check the reads and compare them with chemistry manual as you suggested. Thank you again for yo…
Comment: Microarray batch correction method suggestions by Sumeet • 0
Thank you @atpoint for your response. However, aim of analysing to generate a matrix with all dataset available after batch correction.
Comment: what should I do if I get a compromised sample of scRNA-seq data? by ATpoint 78k
Agreed. I would just force the cells to 5000 or so, and then proceed with the normal QC. If there's a lot of trash "cells" in the dataset t…
Comment: How to download multiple genome files using command line (MacOS) using datasets by rj.rezwan • 0
you should use the `wild cards` to download all the given above GCF files. Moverover, you can use the commands of `curl` , `wget` and `slow…
Comment: Microarray batch correction method suggestions by ATpoint 78k
This has been asked so many times before. Analyse them separately, then make a statement on reproducibility of results using a meta-analysi…
Comment: Microbial gene coverage from blast result by aanchal.yadav • 0
What is qcovhsp (high scoring segment pair) in BLAST output. Can we use this parameter to calculate the gene coverage?
Answer: Best way to normalize transcript reads data for PCA & correlation and further bi by Jeremy ▴ 860
Scaling the data will give you Z-scores. This is a standard way of preparing data for PCA. I would also suggest trying a center-log-ratio…
Comment: How to resolve the error of protein lacking a stop codon when using GenomeThread by peanut • 0
Thank you for your answer,but after verifying the protein file, it seems there is no problem. Even if there are missing codons, the program…
Comment: Help with gatk CreateSequenceDictionary by Chris ▴ 230
It worked! Thanks Matt!
Comment: Finding human .vcf files online to download by cmdcolin ★ 3.4k
i can't really tell you why your code doesn't work if you dont provide it. and, if you describe as much as possible what your goals are, th…
Answer: Help with gatk CreateSequenceDictionary by MatthewP ★ 1.3k
maybe try?: -R /variant_calling/Desktop/demo/supporting_files/hg38/hg38.fa -O /variant_calling/Desktop/demo/supporting_files/hg38/hg3…
Comment: Java error while running HiCDC overview code by Brian Bushnell 20k
Looks like you have corrupt or improperly-formatted input. It's expecting to parse a floating-point number where the word "score" appears.…
Comment: what should I do if I get a compromised sample of scRNA-seq data? by dsull ★ 5.1k
The knee plot is just one type of QC. I'd say just proceed with your analysis and see if you observe anything funky (analysis itself is a Q…
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