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Dinh:COMPUTATIONAL/HIV Insertion Site Sequencing
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bowtie mappings: dinh@meangenemachine-desktop:/media/disk/Sam Human MDA Seq Results$ ./bowtie -f -k 5 -v 0 --best hg18 HIV1_ALL_2008_GENOME_DNA_Primer_File_Clean.fa -t -S HIV1_ALL_2008_GENOME_DNA_Primer_File_vHuman_OUT.sam Time loading forward index: 00:00:01 Time for 0-mismatch search: 00:00:00 # reads processed: 11683 # reads with at least one reported alignment: 15 (0.13%) # reads that failed to align: 11668 (99.87%) Reported 15 alignments to 1 output stream(s) Time searching: 00:00:01 Overall time: 00:00:01 dinh@meangenemachine-desktop:/media/disk/Sam Human MDA Seq Results$ ./bowtie -f -k 5 -v 0 --best hg18 HIV2_ALL_2008_GENOME_DNA_Primer_File_Clean.fa -t -S HIV2_ALL_2008_GENOME_DNA_Primer_File_vHuman_OUT.sam Time loading forward index: 00:00:02 Time for 0-mismatch search: 00:00:00 # reads processed: 9682 # reads with at least one reported alignment: 0 (0.00%) # reads that failed to align: 9682 (100.00%) No alignments Time searching: 00:00:02 Overall time: 00:00:02 dinh@meangenemachine-desktop:/media/disk/Sam Human MDA Seq Results$ ./bowtie -f -k 5 -v 0 --best hg18 SIV_ALL_2008_GENOME_DNA_Primer_File_Clean.fa -t -S SIV_ALL_2008_GENOME_DNA_Primer_File_vHuman_OUT.sam Time loading forward index: 00:00:01 Time for 0-mismatch search: 00:00:00 # reads processed: 5431 # reads with at least one reported alignment: 22 (0.41%) # reads that failed to align: 5409 (99.59%) Reported 98 alignments to 1 output stream(s) Time searching: 00:00:01 Overall time: 00:00:01
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