Hi ,
i'm running the following code to align two primer pair files to my database.
The output looks like this...
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.
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
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
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
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
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