Difference between revisions of "Detonate"

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There are two option with an associated prefix: '''-p''' and  '''--transcript-length-parameters'''. The rest are all positional
 
There are two option with an associated prefix: '''-p''' and  '''--transcript-length-parameters'''. The rest are all positional
 
* -p 8, this refers to the number of threads the program run will use. In this case 8.
 
* -p 8, this refers to the number of threads the program run will use. In this case 8.
* --transcript-length-parameters, a filename and the output of the previous '''rsem-eval-estimate-transcript-length-distribution''' command.
+
* --transcript-length-parameters, a filename contianing the output of the previous '''rsem-eval-estimate-transcript-length-distribution''' command.
 +
* The next option is a comma seperated list of the raw reads used to assebmle the de-novo transcriptome in the first place.
  
 +
It's best to wrap this command in a job submission script as follows:
 +
 +
#!/bin/bash
 +
#$ -V
 +
#$ -cwd
 +
#$ -j y
 +
#$ -S /bin/bash
 +
#$ -q highmemory.q
 +
#$ -pe multi 8
 +
rsem-eval-calculate-score -p $NSLOTS --transcript-length-parameters outputld.txt $(cat fq.lst |tr '\n' ',') <denovassemblyname.fa> <output_prefix> <length_of_short_reads>
  
 
=Links=
 
=Links=
 
[http://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0553-5 The published paper describing Detonate]
 
[http://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0553-5 The published paper describing Detonate]

Revision as of 14:34, 30 January 2017

Introduction

Quality evaulation of a de-novo transcriptome assembly from the creators of RSEM (Deweylab). It was designed to answer the shortcomings in the N50 score typically used to evaluate assembly. It is a much more comprehensive quality evaluation, requiring as input, no only the de-novo assembly, but all the raw reads that were used to assemble it.

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.

Next the RSEM-EVAL score can be calculated. There is one executable for this, and it has various options. Executing

rsem-eval-calculate-score --help

will allow you view them.

The standard usage example is:

rsem-eval-calculate-score -p 8 --transcript-length-parameters human.txt /data/reads.fq assembly1.fa assembly1_rsem_eval 76

Explanation: There are two option with an associated prefix: -p and --transcript-length-parameters. The rest are all positional

  • -p 8, this refers to the number of threads the program run will use. In this case 8.
  • --transcript-length-parameters, a filename contianing the output of the previous rsem-eval-estimate-transcript-length-distribution command.
  • The next option is a comma seperated list of the raw reads used to assebmle the de-novo transcriptome in the first place.

It's best to wrap this command in a job submission script as follows:

  1. !/bin/bash
  2. $ -V
  3. $ -cwd
  4. $ -j y
  5. $ -S /bin/bash
  6. $ -q highmemory.q
  7. $ -pe multi 8

rsem-eval-calculate-score -p $NSLOTS --transcript-length-parameters outputld.txt $(cat fq.lst |tr '\n' ',') <denovassemblyname.fa> <output_prefix> <length_of_short_reads>

Links

The published paper describing Detonate