VascoElbrecht's video: Downloading SRA data with the SRA toolkit FastQC and import into Geneious Part 3

We have identified the NGS data in the NCBI SRA, and now it's time to download the file using the command line application SRA toolkit. We also make a quick quality check of the HiSeq sequence data and the import the 11 million reads into Geneious. 0:09 Download and install the NCBI SRA toolkit to download the SRA data http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software 0:44 Download the SRA file (SRR1145747) using: "sratoolkit.2.4.2-mac64/bin/./prefetch SRR1145747" 2:10 Convert the SRA file to a fastQ file which can be imported into Geneious and other Programs using: "sratoolkit.2.4.2-mac64/bin/./fastq-dump SRR1145747" 3:46 Check the data quality of the NGS data using the program FastQC available here: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ 4:28 Import the fastQ file into geneious 6:42 Data subsetting, you don not want to use all 11 million sequences, computation will take forever. 500.000 will be enough for the beginning. 7:24 Extract forward and reverse sequence from the 500k reads, at the moment they are concatenated and can't be assembled like this (The PE reads don't have overlap). Next Video: Extracting mitochondrial reads using complete MT genomes as references!