|Plant Bioinformatics Vol 3 RNA-Seq Tutorial
|Oct 21, 2022
|An end-to-end RNA-seq analysis using the Kallisto and Sleuth, emphasizing reproducibility features of the CyVerse platforms
|RNASeq using VICE
|Dec 06, 2019
|Perform RNAseq differential expression analysis using Read Mapping and Transcript Assembly (RMTA) and Rstudio-DESEq2 apps
|Assemble a Genome Using SOAPdenovo
|Dec 19, 2019
|Commonly used procedure for de novo whole genome assembly of Illumina reads using the DE: Assemble reads, Assess assembly
|Cluster Orthologs and Paralogs and Assemble Custom Gene Sets
|Dec 11, 2019
|Input entire protein-encoding gene or transcript repertoires from genomes of interest, and cluster homologs (orthologs and paralogs), then query clusters to assemble gene sets based on presence/absence and copy number.
|RNA-Seq with Kallisto and Sleuth
|Nov 04, 2019
|Kallisto is a quick, highly-efficient software for quantifying transcript abundances in an RNA-Seq experiment. Sleuth is designed to analyze and visualize the Kallisto results in R.
|Oct 25, 2019
|Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
|Genome Annotation with MAKER
|Oct 09, 2019
|This tutorial is a step-by-step guide for using SciApps to perform MAKER based annotation
|Evaluate and Pre-Process Sequencing Reads
|Jan 05, 2018
|Clean and filter Illumina reads using DE apps.
|Taxonomic Name Resolution Service (TNRS)
|Dec 05, 2017
|Become familiar with TNRS to identify, correct, and update scientific names of plants.
|Submit High-throughput Sequencing Reads to NCBI Sequence Read Archive (SRA)
|Dec 04, 2017
|The SRA is a canonical repository for sequencing data generated by high-throughput instruments. The CyVerse submission pipeline allows you to directly submit your data into an SRA-linked BioProject.
|Evaluate High-throughput Sequencing Reads with FastQC
|Aug 01, 2017
|FastQC is a popular tool for evaluating the quality of high-throughput sequencing reads such as from Illumina and PacBio.
|Aug 01, 2017
|An automated quality control analysis tool for a single and paired-end high-throughput sequencing data (HTS) generated from Illumina sequencing platforms
|Import data from NCBI SRA using the Discovery Environment
|Apr 04, 2017
|The NCBI Sequence Read Archive (SRA) is a repository for high-throughput sequencing reads. These are valuable data for novel analysis and reuse. You can directly import data from SRA into your Data Store using a Discovery Environment app.
|Discover Variants Using SAM Tools
|Oct 11, 2016
|Detect and call variants from sequence reads using Bowtie and SAM Tools.
|Filter, Trim, and Process High-throughput Sequencing Reads with Trimmomatic
|Sep 15, 2016
|Trimmomatic is a popular application for filtering and trimming high- throughput sequencing reads. Several functions can remove populations of low quality reads, remove sequencing adaptors, and trim low-quality regions of individual reads.
|Characterizing Differential Expression With RNA-Seq (Without Reference Genome)
|Jul 21, 2015
|Identify changes in gene expression levels between at least two sequenced transcriptome samples (18 separate tutorials)
|BLAST a Transcriptome
|May 11, 2016
|Reduce number of transcripts and level of redundancy in an assembled transcriptome, and identify coding sequences that can be submitted to BLASTP searches.
|QIIME-1.9.1 for the DE
|Apr 12, 2016
|QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
|Jan 04, 2016
|Gain familiarity with a commonly used procedure for de novo whole genome assembly of Illumina reads using the DE.
|Genome-wide Association Study (GWAS) Using a Genotyping-by-sequencing Approach
|Sep 27, 2012
|Learn to identify genetic variants that are associated with a trait.