Daniel:Notebook/GenomeMiner/2013-8-19
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HL155
Redoing analysis using Phred 64
Creating build index
bowtie2-build -f Probelist_all.fa hrcp_probesequences &
Running Bowtie 2 with Phred 64 flag
bowtie2 -x hrcp_probesequences -U s_2_1_Indx12.txt,s_2_1_Indx53.txt,s_2_1_Indx54.txt,s_2_1_Indx04.txt,s_2_1_Indx03.txt,s_2_1_Indx05.txt,s_2_1_Indx02.txt, s_2_1_Indx13.txt,s_2_1_Indx01.txt,s_2_1_Indx55.txt,s_2_1_Indx49.txt,s_3_1_Indx11.txt,s_3_1_Indx10.txt,s_2_1_Indx56.txt, s_2_1_Indx52.txt,s_3_1_Indx12.txt,s_2_1_Indx11.txt,s_2_1_Indx50.txt --phred64 -S hrcp_fullindex_samout_p64.out
Results:
71613792 reads; of these: 71613792 (100.00%) were unpaired; of these: 50674903 (70.76%) aligned 0 times 19321427 (26.98%) aligned exactly 1 time 1617462 (2.26%) aligned >1 times 29.24% overall alignment rate