I'm using staden package 1.6, in addition to phred and phrap as basecaller and assembly engine, to assemble sequences obtained with transposon taggin strategy on fosmid clones. Up to date, all has worked fine but lastly, for the most of the sequences, I get this error massage during pregap4 assembly:
Tue 09 Jan 14:20:16 2007 invalid AP line in 'FILENAME.exp.ph'.
In this way, e.g. 126 out of 190 sequences are refused, even if the quality seems to be good.
What is the error message about? What can I do?
I solved the problem.
Sequence names should be shorter than 30 chars.
I have been given files with very long names, only some of which is unique. What is the best way to get them cut down to unique names suitable for staden?