[maker-devel] how the maker2 pipeline deal with a Ns sequence

[Quanwei Zhang]

Hello:

I wonder how the maker2 pipeline deals with a 1kb or 100bp NN sequences in
a scafold, especially when such sequences within a gene region?

Recently, we improved a rodent genome. However, at a few certain regions we
filled the gap with both sequences and Ns sequences. We found some
predicted genes in the old assembly lost in our new assembly. By looking
deep into the region, the gene region in the new assembly highly match the
old assembly at both ends of the gene, where covered most predicted coding
sequences (predicted in the old assembly). The only difference is shown in
the middle of the gene with some new sequence and Ns sequences. Attached in
the alignments between sequence in the old and new assembly in the gene
region (Y coordinate shows the new assembly).

Many thanks and Merry Christmas

Best
Quanwei
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