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Old 07-20-2015, 06:42 AM   #1
danova
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Location: France

Join Date: Sep 2010
Posts: 27
Default Count number of genes matched for each primer pair - Bowtie2 - samtools

HI,
I'm running the following bowtie2 command to identify proper pairs matching my database. I have added the no-mixed since i only want proper pairs (no single mates). No mismatches for the moment as specified by -N0

ALL_forward.fna: A fasta list of forward primers
ALL_reverse.fna : A fasta list of reverse primers

Code:
bowtie2  -N0 -a  --no-mixed --fr  --minins 450 --maxins 1500 -x database -1 ALL_forward.fna -2 ALL_reverse.fna  > out.sam
Here is the output. In this case i can see that primer f_109 and r_209 have full matches to different genes of my database. How can i count how many genes are targetted by each primer pair.

Ideally the ouput should be:
Primer-pair Nb_hits Seqs
f_109-r_209 5 ATAAGCTCACGA-CGGAACTGCACG

which means that primer pair f_109-r_209 has targets 5 genes in my database and the output sequences.

Since i have different primers how can i get this information from the output ??

Code:
f_109   99      JQ337711.1.1426 112     0       12M     =       578     478     ATAAGCTCACGA    IIIIIIIIIIII    AS:i:-6 XS:i:-6 XN:i:0  XM:i:1
        XO:i:0  XG:i:0  NM:i:1  MD:Z:6C5        YS:i:-6 YT:Z:CP
r_209   147     JQ337711.1.1426 578     0       12M     =       112     -478    CGGAACTGCACG    IIIIIIIIIIII    AS:i:-6 XS:i:-6 XN:i:0  XM:i:1
        XO:i:0  XG:i:0  NM:i:1  MD:Z:11T0       YS:i:-6 YT:Z:CP
f_109   355     JX227029.1.1518 168     0       12M     =       645     489     ATAAGCTCACGA    IIIIIIIIIIII    AS:i:-6 XS:i:-6 XN:i:0  XM:i:1
        XO:i:0  XG:i:0  NM:i:1  MD:Z:6C5        YS:i:-6 YT:Z:CP
r_209   403     JX227029.1.1518 645     0       12M     =       168     -489    CGGAACTGCACG    IIIIIIIIIIII    AS:i:-6 XS:i:-6 XN:i:0  XM:i:1
        XO:i:0  XG:i:0  NM:i:1  MD:Z:2A9        YS:i:-6 YT:Z:CP
thanks for any help,

Last edited by danova; 07-20-2015 at 07:50 AM.
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