Daniel:Notebook/GenomeMiner/2013-9-12

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Revision as of 20:29, 12 September 2013 by >Djacobse (→‎Mock HL155 (Started 9/9/2013))
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Mock HL155 (Started 9/9/2013)

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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

Alignment Results

2959000 reads; of these:
 2959000 (100.00%) were unpaired; of these:
   0 (0.00%) aligned 0 times
   2953000 (99.80%) aligned exactly 1 time
   6000 (0.20%) aligned >1 times
100.00% overall alignment rate

So it looks like even with indisputable base quality and sequences, about 0.2% of sequences are so close that bowtie2 thinks they can be several sequences.

Bowtie on Perfect Mock Sequence Data(Started 09/11/2013)

Using Matt's Perlscript: File:Imp count mismatch.txt

Error Rate: 0
Error Rate of Insertions: 0
Error Rate of Deletions: 0
Error Rate of Substitutions: 0