Difference between revisions of "Detonate"
Line 32: | Line 32: | ||
After de-novo assembly of your transcriptome, the first step is | After de-novo assembly of your transcriptome, the first step is | ||
− | rsem-eval-estimate-transcript-length-distribution <contigs.fasta> | + | rsem-eval-estimate-transcript-length-distribution <contigs.fasta> <outputld.txt> |
<ins>Explanation</ins>: | <ins>Explanation</ins>: | ||
* rsem-eval-estimate-transcript-length-distribution, a perl script | * rsem-eval-estimate-transcript-length-distribution, a perl script | ||
* <contigs.fasta>, your de-novo assembly | * <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. |
Revision as of 13:27, 30 January 2017
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
- rsem-eval-calculate-score
- rsem-eval-estimate-transcript-length-distribution
- rsem-plot-model
- rsem-build-read-index
- rsem-eval-run-em
- rsem-extract-reference-transcripts
- rsem-parse-alignments
- rsem-preref
- rsem-sam-validator
- rsem-scan-for-paired-end-reads
- rsem-simulate-reads
- rsem-synthesis-reference-transcripts
- ref-eval
- ref-eval
- 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.