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High Throughput Annotation of Modified Ribonucleotides (HAMR) detects modified ribonucleotides based upon their ability to intefere with Watson-Crick base pairing. This leads to reverse transcriptase base misincorporations, which can be detected as mismatches from the reference genome in cDNA-based RNA-seq libraries. HAMR tabulates these mismatches and tests for patterns of mismatches that cannot be explained by: Sequencing errors, Single nucleotide polymorphisms (SNPs) or RNA editing.
In this tutorial, we will be using Cyverse Discovery Environment (DE) public apps for analysis of a sample dataset. Command-line expertise is not required to follow most of this tutorial.
Who to contact if this guide needs fixing. You can also email learning@CyVerse.org
| Maintainer | Institution | Contact |
|---|---|---|
| Reetu Tuteja | CyVerse / UA | reetututeja@cyverse.org |
.. toctree::
:maxdepth: 2
Sample dataset and preprocessing <step1.rst>
Read mapping <step2.rst>
Filter multi-mapping reads and add read groups <step3.rst>
Resolve spliced alignments using GATK <step4.rst>
Running HAMR <step5.rst>
Further reading <step6.rst>
In order to complete this tutorial you will need access to the following services/software
| Prerequisite | Preparation/Notes | Link/Download |
|---|---|---|
| CyVerse account | You will need a CyVerse account to complete this exercise | |CyVerse User Portal| |
We will use the following CyVerse platform(s):
| Platform | Interface | Link | Platform Tour |
|---|---|---|---|
| Data Store | GUI/Command line | |Data Store| | |Data Store Guide| |
| Discovery Environment | Web/Point-and-click | |Discovery Environment| | |Discovery Environment Guide| |
Discovery Environment App(s):
Fix or improve this documentation
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