Modify Scaffolds to create a New reference

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4.7 years ago

ben.blais ▴ 10

Hello everyone, I would like to ask you about a current problem which I face. Indeed, I got scaffolds from contigs. Then, I used Blat to compare these scaffolds to a near reference, and then visualize this alignment with IGV. When viewing, I can see that there are small gaps when aligning the scaffolds on the reference. I would like to know if it is possible to modify these scaffolds and thus to fill the gaps by N in order to create a "new reference"? I hope I have been pretty clear in my comments. Thanks you in advance for any help and wish you an excellent end of the day.