|RNA-Seq with Kallisto and Sleuth
||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.
|Genome Annotation with MAKER
||This tutorial is a step-by-step guide for using SciApps to perform MAKER
|Import data from NCBI SRA using the Discovery Environment
||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.
|Evaluate High-throughput Sequencing Reads with FastQC
||FastQC is a popular tool for evaluating the quality of high-throughput sequencing
reads such as from Illumina and PacBio.
|Filter, Trim, and Process High-throughput Sequencing Reads with Trimmomatic
||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.
|Submit High-throughput Sequencing Reads to NCBI Sequence Read Archive (SRA)
||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.
|Assemble a Genome Using SOAPdenovo
||Commonly used procedure for de novo whole genome assembly of Illumina reads using the DE:
Assemble reads, Assess assembly
|BLAST a Transcriptome
||Reduce number of transcripts and level of redundancy in an assembled transcriptome,
and identify coding sequences that can be submitted to BLASTP searches.
|Characterizing Differential Expression With RNA-Seq (Without Reference Genome)
||Identify changes in gene expression levels between at least two sequenced
transcriptome samples (18 separate tutorials)
|Cluster Orthologs and Paralogs and Assemble Custom Gene Sets
||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.
||Discover Variants Using SAM Tools|
||Detect and call variants from sequence reads using Bowtie and SAM Tools.
|Evaluate and Pre-Process Sequencing Reads
||Clean and filter Illumina reads using DE apps.
|Genome-wide Association Study (GWAS) Using a Genotyping-by-sequencing Approach
||Learn to identify genetic variants that are associated with a trait.
||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.
||Gain familiarity with a commonly used procedure for de novo whole genome assembly of Illumina reads using the DE.
|QIIME-1.9.1 for the DE
||QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
|Taxonomic Name Resolution Service (TNRS)
||Become familiar with TNRS to identify, correct, and update scientific names of plants.