Daniel:Notebook/GenomeMiner/2013-9-9
Mock HL155[edit]
At Dr. Zhang's recommendation Matt and I are working on mock sequencing data to investigate some of the discrepancies from sequencing, specifically why the reverse complement had such a large effect on the results from the MYcroarray data.
Generating the Mock Sequencing Data[edit]
The first run is going to be perfect copies of the sequencing data, since that is the easiest to make.
Sequences are taken from the ones Matt used for analysis on 9/3/2013. Those are taken from the original sequences from Dr. Zhang. They have been changed to the reverse complement and chopped down to 50bp from the 3' end.
Base qualities were extracted from the real sequencing data, specifically sam format (V4S1_bowtie2.sam). Being in sam format, they use the "Illumina 1.8+ Phred+33, raw reads typically (0, 41)" format article on fastq formats. This will alter the settings used in bowtie2 from the normal pipeline Matt and I used.
I used a MATLAB script (MockHl155_Master.m, switch 1) to generate fastq files. Since this was the "perfect version", the sequences were simply copied from the V4S1 file. Base quality, however, was taken from the actual sequencing file and so includes bases of low quality.