small RNAseq pipelines - current status

Created: 2020/09/24 15:19:42 Last modified: 2021/08/03 10:57:21

• Aim: Evaluate the current pipelines available for processing small RNA-seq data

Table of contents

• small RNAseq pipelines - current status
  • Table of contents
  • Pipelines
  • Other things of possible interest
  • Notes

Pipelines

See small RNAseq pipelines for a spreadsheet of pipelines

Other things of possible interest

• Prediction and annotation of tRNA-derived small RNAs here
• A JBrowse plugin to support small RNA visualization here
• A set of tools related to the Rfam (database of non-coding RNA families https://rfam.org/) production pipeline here
• Script to map annotated ncRNAs (and other elements) to a chromosome and visualise here
• HPC-REDItools - A tool for large-scale RNA-editing analysis (RNA-editing is a molecular process through which some cells can make discrete changes to specific nucleotide sequences within an RNA molecule after it has been generated by RNA polymerase)

Notes

• smrnaseq is still the most robust pipeline I’ve come across in terms of:
  • being in a workflow language
  • being specific to both small and non-coding RNA
  • being deployable to cluster/cloud environments
• There are far more pipelines available for RNA-seq data
• There seems to very few pipelines dedicated to both small and non-coding RNA-seq