Daniel:Notebook/GenomeMiner/2013-7-25: Difference between revisions

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>Djacobse
(Created page with "=HL155= Back to Calendar ==Bowtie Indexing== Tried to do some more work on this today, but I realized that I messed up naming the fasta file...")
 
>Djacobse
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Line 32: Line 32:
     1598009 (2.23%) aligned >1 times
     1598009 (2.23%) aligned >1 times
  28.94% overall alignment rate
  28.94% overall alignment rate
Looks like the result was the same, though it should be easier for analysis now.

Revision as of 22:24, 25 July 2013

HL155

Back to Calendar

Bowtie Indexing

Tried to do some more work on this today, but I realized that I messed up naming the fasta files for indexing. I gave all the probes the name "Probe_set1_m", where m was a integer number ranging from 1 to the total number of probes in the set. What I wanted, however, was "Probe_setn_m", where n was a number 1 to 4 indicating which set it was in. I repaired the mistake in the fasta files today. Individually I used this command in vi editor:

:%s/set1/setn/g

Again, n is an integer 2-4.

Then I made the fasta files into index files.

Creating the Index File

 bowtie2-build -f Probelist_Set1.fa,Probelist_Set2.fa,Probelist_Set3.fa,Probelist_Set4.fa hcrp_probeseq

Then bowtie.

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:~/perl$ 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

Looks like the result was the same, though it should be easier for analysis now.