Hi,
Not sure it´s the correct strategy by i´m trying to achieve the following:
1- I have two primers (see below) that map to 16s amplicons and they generate an insert of 1200 to 1400 nt long.
The two primers are described below.
>forward_primer
CCTACGGGNGGCWGCAG
>reverse_primer
GGATTAGATACCCBDGTAGTC
When i try to use bowtie2 to align the two primers to a reference database of different 16S sequences they are supposed to match i only get 600 hits (expected 400000 hits), meaning this primer set will align perfectly to 400000 different sequences of the database.
bowtie2 -f -t -a --no-dovetail --no-contain --no-overlap --no-mixed --fr --minins 800 --maxins 1500 -x 16S_database -1 forward_primer -2 reverse_primer
I have checked the orientation of the primers , -fr is the correct orientation.
It looks too me that bowtie2 handles degenerated primers differently then what i expected. Does anybody know how to improve the alignement of the degenerated primers (-N 1 option does not really improve). ANy idea ???
Not sure it´s the correct strategy by i´m trying to achieve the following:
1- I have two primers (see below) that map to 16s amplicons and they generate an insert of 1200 to 1400 nt long.
The two primers are described below.
>forward_primer
CCTACGGGNGGCWGCAG
>reverse_primer
GGATTAGATACCCBDGTAGTC
When i try to use bowtie2 to align the two primers to a reference database of different 16S sequences they are supposed to match i only get 600 hits (expected 400000 hits), meaning this primer set will align perfectly to 400000 different sequences of the database.
bowtie2 -f -t -a --no-dovetail --no-contain --no-overlap --no-mixed --fr --minins 800 --maxins 1500 -x 16S_database -1 forward_primer -2 reverse_primer
I have checked the orientation of the primers , -fr is the correct orientation.
It looks too me that bowtie2 handles degenerated primers differently then what i expected. Does anybody know how to improve the alignement of the degenerated primers (-N 1 option does not really improve). ANy idea ???
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