Detonate

Introduction

Quality evaulation of a de-novo transcriptome assembly from the creators of RSEM (Deweylab).

Layout

Two main aspects to this program. Also included here are the executables associated

• rsem-eval
  1. rsem-eval-calculate-score
  2. rsem-eval-estimate-transcript-length-distribution
  3. rsem-plot-model
  4. rsem-build-read-index
  5. rsem-eval-run-em
  6. rsem-extract-reference-transcripts
  7. rsem-parse-alignments
  8. rsem-preref
  9. rsem-sam-validator
  10. rsem-scan-for-paired-end-reads
  11. rsem-simulate-reads
  12. rsem-synthesis-reference-transcripts

• ref-eval
  1. ref-eval
  2. ref-eval-estimate-true-assembly

Usage

The detonate module must be loaded beforehand

module load detonate

After de-novo assembly of your transcriptome, the first step is

rsem-eval-estimate-transcript-length-distribution <contigs.fasta> <outputld.txt>

Explanation:

• rsem-eval-estimate-transcript-length-distribution, a perl script
• <contigs.fasta>, your de-novo assembly
• <outputld.txt>, your chosen name for the output text file which will hold the mean and SD of the contig lengths distribution.