|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.