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

@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!

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This video was published on 2014-12-31 00:43:05 GMT by @luckylion on Youtube. VascoElbrecht has total 9.2K subscribers on Youtube and has a total of 63 video.This video has received 140 Likes which are lower than the average likes that VascoElbrecht gets . @luckylion receives an average views of 34.9K per video on Youtube.This video has received 10 comments which are lower than the average comments that VascoElbrecht gets . Overall the views for this video was lower than the average for the profile.

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