The plan for this week is to practice the usage of Galaxy.
The basic protocol is:
- Use FasterQ Download to transfer the SRA entry SRR3997516
- Use FastQC to generate a quality control report
- Use NCBI Genomes Datasets to transfer genome assembly GCF_000371365.1, selecting at least FASTA and GFF3 formats
- Use HISAT2 to map each read from the FASTQ files into the genome in FASTA format. You may need to look at “Show Hidden” and make the individual FASTQ files “unhidden”.
That is what we said. If you finished this, you may try the next step. Use StringTie to combine the output of HISAT2 (in BAM format) with the genome GFF3 file.
To deliver you must share your “history” with me.