vector contamination - extract readings ?!

arnim wiezer arnim at tower.goe.net
Fri Feb 21 04:26:53 EST 2003


Good morning NG !

We are working on a quite huge project with abount 70,000 reads. Yesterday
we noticed that something with the vectorclipping went wrong, so that we
have contaminations of sequencing vector in most of the contigs.

Does anyone have an idea how to get rid of this ? My idea was to extract
all the reads, process these .exp files with pregap and than put them
together with directed assembly. But this resulted in a complete
missassembly or a crash of gap4 :-(

Any help appreciated :-)

Arnim





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