4 answers
I'd recommend bbduck from the BBMap suite. It has included a lot of adapters and primer sequences, is very fast, and you can trim next to adapters also low-quality tails. Additionally, it is keeping your paired-end data in the correct order (if one read is removed, the other is removed too).
Trim Galore worked for me.
http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
cutadapt is also a nice one.
To Juke-34. I have tried, but seems I could get the 3´primers cut off, I use the command cutadapt -a <reverse primer="" sequence=""> o <output name=""> directory/input file for the reverse primer sequence I hoped to cut, I tried the either the exact sequence of from 5´to 3´, or the reverse complementary one (the same as reverse primer as we order), both did not work. So any suggestions?
Thanks Ramona
For reverse primer I guess the parameter is something like -A instead of -a. Did you read carefully the User Guide documentation ?
Everything is well explained with examples.
for the 5' you need to use -g instead of -a. also sometimes the 5' adapters have more mistakes, so you can change the error rate (-e 0.2 allows 20% mistakes. 10% is the default)
for the 5' you need to use -g instead of -a. also sometimes the 5' adapters have more mistakes, so you can change the error rate (-e 0.2 allows 20% mistakes. 10% is the default)
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