Hi guys, I am trying to trim my primer sequences off my sequence data. I wrote the command with cutadapt.
cutadapt -g F-primer sequence -o output file name directory of input file/input file name
it could cut the forward primer off. but if I use the same command for reverse primers
cutadapt -a R-primer sequence -o output file name directory of input file/input file name
it did not work. I tried to put the reverse complementary sequence of the 3´ sequence of the primer, it did not work either. If I merge the 2 reads and do the cutadapt,
cutadapt -a <3´sequence> -g <forward primer sequence> -o <output file name> directory of input file/input file name
neither works. So I wonder if anyone can give me some suggestions on how to make the right command, or is there any better software to use to trim the primer sequences?