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Old 07-22-2015, 02:34 AM   #1
danova
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Location: France

Join Date: Sep 2010
Posts: 27
Default Bowtie output question

Hi ,
i'm running the following code to align two primer pair files to my database.

Code:
bowtie  -f -t -p 10 -a --best --pairtries 1000 -n0  --fr  --minins 600 --maxins 2500 Bact_archea  -1 fortest.fa -2 revtest.fa
The output looks like this...
Code:
f_1/1   +       GQ246403.1.1498 0       AGAGTTTGATCATGGC        IIIIIIIIIIIIIIII        79309   
r_2/2   -       GQ246403.1.1498 1479    AAGTCGTAACAAGGTA        IIIIIIIIIIIIIIII        79309   
f_1/1   +       JF775628.1.1474 0       AGAGTTTGATCATGGC        IIIIIIIIIIIIIIII        79309   
r_2/2   -       JF775628.1.1474 1455    AAGTCGTAACAAGGTA        IIIIIIIIIIIIIIII        79309
What I look at this output i know that i have 79309 other hits in the database. This very helpful information that i want.

Now , i have tried to use the sam output by using the same command adding the "-S" tag . The sam output looks like this.

Code:
@HD     VN:1.0  SO:unsorted
@PG     ID:Bowtie       VN:1.1.2        CL:"bowtie --wrapper basic-0 -f -t -p 1 -a --best --pairtries 1000 -n0 --fr --minins 600 --maxins 2500 Bact_archea -1 fortest.fa -2 revtest.fa -S"
f_1     99      GQ246403.1.1498 1       255     16M     =       1480    1495    AGAGTTTGATCATGGC        IIIIIIIIIIIIIIII        XA:i:0  MD:Z:16 NM:i:0
r_2     147     GQ246403.1.1498 1480    255     16M     =       1       -1495   AAGTCGTAACAAGGTA        IIIIIIIIIIIIIIII        XA:i:0  MD:Z:16 NM:i:0
f_1     99      JF775628.1.1474 1       255     16M     =       1456    1471    AGAGTTTGATCATGGC        IIIIIIIIIIIIIIII        XA:i:0  MD:Z:16 NM:i:0
r_2     147     JF775628.1.1474 1456    255     16M     =       1       -1471   AAGTCGTAACAAGGTA        IIIIIIIIIIIIIIII        XA:i:0  MD:Z:16 NM:i:0
f_1     99      EU265948.1.1520 1       255     16M     =       1502    1517    AGAGTTTGATCATGGC        IIIIIIIIIIIIIIII        XA:i:0  MD:Z:16 NM:i:0
I don't have the total number of alignments as i had before (79309). Is there a way to get the number of alignments found.

Since my forward and reverse primers contains several primer pairs i want to get the total number of alignments per pair.

Of course I can do it from my first output file but since it seems that sam format is a standard i was wondering how to get the same information ??

Thanks,
david
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