Daniel:Notebook/GenomeMiner/2013-7-18
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HL155
=Bowtie Indexing
Using the fasta files I created Tuesday, I created an index file.
Creating the Index File
bowtie2-build -f Probelist_Set1.fa,Probelist_Set2.fa,Probelist_Set3.fa,Probelist_Set4.fa hcrp_probeseq
Test Bowtie2 Command Line
bowtie2 -x hcrp_probeseq -U s_2_1_Indx12.fq,s_2_1_Indx53.fq,s_2_1_Indx54.fq -S testSAMout &
That seemed to go well enough (I think), so I did the full command:
Bowtie2
bowtie2 -x hcrp_probeseq -U s_2_1_Indx12.fq,s_2_1_Indx53.fq,s_2_1_Indx54.fq,s_2_1_Indx04.fq,s_2_1_Indx03.fq, s_2_1_Indx05.fq_2_1_Indx02.fq,s_2_1_Indx13.fq,s_2_1_Indx01.fq,s_2_1_Indx55.fq,s_2_1_Indx49.fq,s_3_1_Indx11.fq, s_3_1_Indx10.fq,s_2_1_Indx56.fq,s_2_1_Indx52.fq,s_3_1_Indx12.fq,s_2_1_Indx11.fq,s_2_1_Indx50.fq -S hrcp_fullindex_samout.out &