Daniel:Notebook/GenomeMiner/2013-9-12
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Mock HL155 (Started 9/9/2013)
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 Counts: 2955000 perfect, 0 with error
So this is expected from the sequencing data with no errors.