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Old 02-08-2017, 01:18 PM   #1
Location: Mountain Grove, MO, USA

Join Date: Apr 2014
Posts: 29
Default reads align but contigs do not??

Here is something that puzzles me:
I have 4000 reads that align to my reference genome. I can visualize them, they cover maybe 80 % or a little more of the reference sequence.
I assemble these reads into contigs, get something like 160 contigs. ok.
however, when I try to align these contigs, only 27 of them still match my reference.
huh? how is that possible?
Any thoughts?
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