Daniel:Notebook/GenomeMiner/2013-9-11

From ZhangLabWiki
Jump to navigation Jump to search

Mock HL155 (Started 9/9/2013)[edit]

Back to Calendar

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