Introduction ~~~~~~~~ Rnaquast
is a quality assessment tool for de novo transcriptome assemblies.
- 2.2.1
Commands ~~~~~~~ - rnaQUAST.py
Note
When reference genome and gene database are unavailable, users can also use BUSCO
and GeneMarkS-T
in rnaQUAST pipeline. Since GeneMarkS-T
requires the license key, users may need to download your own key, and put it in your $HOME. rnaQUAST is also capable of calculating various statistics using raw reads (e.g. database coverage by reads). To use this, you will need use STAR
in the pipeline. BUSCO
, GeneMarkS-T
, and STAR
have been installed, and the directories of their exectuables have been added to $PATH. Users do not need to load these modules. The only module required is rnaquast
itself.
You can load the modules by:
module load biocontainers
module load rnaquast
Example job ~~~~~ .. warning:: Using #!/bin/sh -l
as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash
instead.
To run Rnaquast on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=rnaquast
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers rnaquast
rnaQUAST.py -t 12 -o output \
--transcripts Trinity.fasta idba.fasta \
--reference Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa \
--gtf Saccharomyces_cerevisiae.R64-1-1.75.gtf
rnaQUAST.py -t 12 -o output2 \
--reference reference.fasta \
--transcripts transcripts.fasta \
--left_reads lef.fastq \
--right_reads right.fastq \
--busco fungi_odb10