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]

Back to Calendar

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.