JoseBlanca
commented
13 years ago From the MIRA mailing list.
So the cross_match + smalt seems to have done the trick.
When I BLAST the adapters against the created contigs no hits are found.
In the repeat histogram, the maximum repeat is 324 as opposed 40,000.
And on top of it. The N50 is 1150 as compared to the 850 before and the largest contig is 8000, as opposed to 4000.
WASH RINSE and REPEAT!
Sincerely yours,
Robin
Sometimes exonerate does't find adaptors shorter than 20 nucleotides. We should solve this problem maybe using another aligner: ssaha??