SFF file - primers

[pingu]

Hello!
I am using 454 Roche Junior, I have few questions about reads of sff file.
I have splitted a SFF file into individual SFF file (according to their MIDs), I don't understand if I have to do also remove primers in the reads or if they are already removed.
Please could you explain me the structure of a read in general?
Thank you in advance

[flxlex]

Primers should already be removed, both the primers that are used for sequencing and the MID sequences. When in doubt, you could use prinseq, it will try to detect adaptor sequences. http://edwards.sdsu.edu/cgi-bin/prinseq/prinseq.cgi.

[pingu]

Thank you very much for your response. I have another question: is it a problem if my amplicon is longer than final read and it is possibile that the end (3') of my read is incomplete?

Thank you in advance for your attention!

[flxlex]

A problem for what? Depends on your further analysis steps, I guess?