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?
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?
Comment