Hi all,
My experiment consists in a paired end Illumina de novo assembly having a
similar reference genome.
After doing first a mapping afterwards I got the debrislist file and four
different types of reads where found.
NO_OVERLAP
CLIP_BAD_SOLEXA_END
CLIP_KNOWNADAPTORRIGHT
CLIP_POLYBASEATEND
CLIP_PROPOSEDENDCLIP
NOT_MAPPED
I wonder which of the reads should I use for performing a de novo analysis
in order to detect sequences not present in the reference strain. I think I
should just use "NO_OVERLAP" and "NOT_MAPPED" reads. Is this correct?
What is the difference between this two types of sequences?
Thanks in advance
