Analyses
The rawdata obtained were quality checked by using the software FastQC. The commands used for this step can be seen in the code page section fastaqc. Thereafter, a scaffold was chosen to continue the other analyses with. The scaffold 10 was chosen and a script was done using the program multiqc (the script can be seen in the code page section multiqc) so that the quality reports for scaffold 10 were gathered into a summary report instead. The generated summary reports from illumina, pacbio and the trancriptome were downloaded.
Illumina quality report
Pacbio quality report
Transcriptomic quality report
Trimmed:
Untrimmed:
Trimmed data that previously was untrimmed:
The pacbio scaffold 10 data was assembled using the program canu. A script was made and can be seen in the code page section canu and was runned with the command sbatch.
The untrimmed transcriptomic data was trimmed using the program trimmomatic. A script was made and can be seen in the code page section trimmomatic and was runned with the command sbatch.
Mapping of the illumina reads (scaffold 10 1P and scaffold 10 2P) and the assembled pacbio scaffold 10 data was done with the program BWA so that the assembly thereafter could be corrected with the illumina reads. The code can be seen in the code page section mapping with bwa and the script was runned with the command sbatch.
Improvement of the assembly was made by using the program pilon that required the assembly as imput as well as the aligned bam file from the previous step. A script was made and can be seen in the code page section pilon.
Quality assessment was made with quast. The script can be seen in the code page section quast.
The program repeatmasker was used on the fasta file obtained from the pilon analysis. This program was used in order to improve the prediction accuracy by masking the repeats in the genome. A script was made and can be seen in the code page section repeatmasker.
The program star was used in order to map the trimmed RNA-seq reads to the assembled masked genome. A script was made and can be seen in the code page section star.