Daniel:Notebook/GenomeMiner/2013-9-11: Difference between revisions
Jump to navigation
Jump to search
>Djacobse |
>Djacobse |
||
Line 21: | Line 21: | ||
'''Convert Sam to Bam and Sort''' | '''Convert Sam to Bam and Sort''' | ||
samtools view -bS mockseq_v4s1_perfect.sam | samtools sort - mockseq_v4s1_perfect | 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 |
Latest revision as of 00:23, 12 September 2013
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