Daniel:Notebook/GenomeMiner/2013-9-12

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Revision as of 18:19, 12 September 2013 by >Djacobse (Created page with "=Mock HL155 (Started 9/9/2013)= Back to Calendar ==Bowtie on Perfect Mock Sequence Data with Perfect...")
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Mock HL155 (Started 9/9/2013)

Back to Calendar

Bowtie on Perfect Mock Sequence Data with Perfect Base Qualities

Based on the results from yesterday I'm seeing what kind of alignment bowtie2 does on perfect sequences with perfect base qualities. Yesterday's sequences were direct copies of the .fa file, but they used base qualities randomly picked from the original sequencing data. These base qualities are all I (an extremely high quality score for phred33).

Generated using MATLAB (MockHL155_Master, Switch 3)

scp to Genome Miner

scp V4S1_mockseq_perfseqbqual.fq djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/mockseq/

bowtie2

bowtie2 -x bbuild_v4s1 -U v4s1_mockseq_perfseqbqual.fq --phred33 -S mockseq_v4s1_perfseqbqual.sam