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
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 ??
thanks for any help,
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
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