Dinh:COMPUTATIONAL/HIV Insertion Site Sequencing

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Revision as of 23:24, 1 December 2009 by >Dinh (New page: 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_GE...)
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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

  1. reads processed: 11683
  2. reads with at least one reported alignment: 15 (0.13%)
  3. 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

  1. reads processed: 9682
  2. reads with at least one reported alignment: 0 (0.00%)
  3. 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

  1. reads processed: 5431
  2. reads with at least one reported alignment: 22 (0.41%)
  3. 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