Daniel:Notebook/GenomeMiner/2013-9-11
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Mock HL155 (Started 9/9/2013)[edit]
Bowtie on Perfect Mock Sequence Data[edit]
Bowtie Build
bowtie2-build -f V4S1.fa bbuild_v4s1
Bowtie2
bowtie2 -x bbuild_v4s1 -U v4s1_mockseq_perfect.fq --phred33 -S mockseq_v4s1_perfect.sam
Results
2959000 reads; of these: 2959000 (100.00%) were unpaired; of these: 0 (0.00%) aligned 0 times 2952904 (99.79%) aligned exactly 1 time 6096 (0.21%) aligned >1 times 100.00% overall alignment rate
Convert Sam to Bam and Sort
samtools view -bS mockseq_v4s1_perfect.sam | samtools sort - mockseq_v4s1_perfect
Filter and Convert Back to Sam
samtools view -h -F 4 -q 8 mockseq_v4s1_perfect.bam > mockseq_v4s1perfect_sortfilt.sam
Replace Matched Pairs with Equals
samtools calmd -eS mockseq_v4s1perfect_sortfilt.sam V4S1.fa > mockseqv4s1perf_sortfilteq.sam