Daniel:Notebook/GenomeMiner/2013-9-9: Difference between revisions

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(Created page with "=Mock HL155= 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 rever...")
 
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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 [[Daniel:Notebook/GenomeMiner/2013-9-5#Results|large effect]] on the results from the MYcroarray data.
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 [[Daniel:Notebook/GenomeMiner/2013-9-5#Results|large effect]] on the results from the MYcroarray data.
==Generating the Mock Sequencing Data==
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 [[Daniel:Notebook/GenomeMiner/2013-9-3|analysis on 9/3/2013]].  Those are taken from the [[Daniel:Notebook/HiResChrPaint#Probe Design|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 (NAME OF SAMFILE).  Being in sam format, they use the "Illumina 1.8+ Phred+33,  raw reads typically (0, 41)" format [http://en.wikipedia.org/wiki/FASTQ_format#Encoding].

Revision as of 23:11, 9 September 2013

Mock HL155

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

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 (NAME OF SAMFILE). Being in sam format, they use the "Illumina 1.8+ Phred+33, raw reads typically (0, 41)" format [1].