I'm currently working on some sequencing and I have a few problems in my assembly. How do I resolve the problems below?
Please take a look at attached Fig1.jpg and Fig3.jpg. These look to me like they are not supposed to assemble together because of the copy number variation in the repeat, but the upstream and downstream matches are wonderful for quite a good length.
Now, please take a look at Fig2.jpg. Is this a SNP? How do I decide which nucleotide for the consensus?
Thanks for your help.