Daniel:Notebook/GenomeMiner/2013-7-18: Difference between revisions
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[[Daniel:Notebook/GenomeMiner|Back to Calendar]] | [[Daniel:Notebook/GenomeMiner|Back to Calendar]] | ||
==Bowtie Indexing= | ==Bowtie Indexing== | ||
Using the fasta files I created [[Daniel:Notebook/GenomeMiner/2013-7-16|Tuesday]], I created an index file. | Using the fasta files I created [[Daniel:Notebook/GenomeMiner/2013-7-16|Tuesday]], I created an index file. | ||
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bowtie2-build -f Probelist_Set1.fa,Probelist_Set2.fa,Probelist_Set3.fa,Probelist_Set4.fa hcrp_probeseq | bowtie2-build -f Probelist_Set1.fa,Probelist_Set2.fa,Probelist_Set3.fa,Probelist_Set4.fa hcrp_probeseq | ||
''Test Bowtie2 Command Line''' | '''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 & | 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 & | |||
Output: | |||
djacobse@genome-miner:~/HL155/130628_HL155$ 71613792 reads; of these: | |||
71613792 (100.00%) were unpaired; of these: | |||
50886517 (71.06%) aligned 0 times | |||
19129266 (26.71%) aligned exactly 1 time | |||
1598009 (2.23%) aligned >1 times | |||
28.94% overall alignment rate | |||
So, yeah. |
Latest revision as of 20:53, 22 July 2013
HL155[edit]
Bowtie Indexing[edit]
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 &
Output:
djacobse@genome-miner:~/HL155/130628_HL155$ 71613792 reads; of these: 71613792 (100.00%) were unpaired; of these: 50886517 (71.06%) aligned 0 times 19129266 (26.71%) aligned exactly 1 time 1598009 (2.23%) aligned >1 times 28.94% overall alignment rate
So, yeah.