Primers Within Reads

Question

[Sam]

How can I remove primers from reads. Note: reads have small letters attached on both ends,are those primers?

[Eric Fournier]

You will need to provide a lot more details to get an informative answer to your question. What sequencing technology are you using? Which formats are your reads in? Were your reads pre-processed?

[Michael]

I think you are talking about adapter sequence, and possibly you are using 454? We shouldn't have to guess though, so I recommend you tell us all the facts. Just in case, adapter sequences will be clipped automatically when converting sff to fasta using the gs* tools coming with the roche sequencer.

Answer 1

[Istvan Albert]

For data in FASTQ format the fastx toolkit offers some options. If your data is in other formats please edit your question and specify what you need.