| 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. |
| Kallisto-0.42.3-INDEX-QUANT-PE |
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. |
| HTSeqQC |
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. |
| mini SOAPdenovo |
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. |