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Remove vector sequences

I sequenced BAC DNA using Oxford Nanopore MinION. These are large ranging from 1000 to 200,000 basepairs long raw sequences. I want to remove the vector sequence attached to the BAC sequence. The vector sequence is ~7500 base pairs long. I used stand alone BLAST and I got only 64 BLAST hits, this is unexpected. I have a total of 272849 BAC raw sequences (from nanopore) in my input file. So, I can't believe the BLAST result. I want to trim vector sequence before I assemble. I appreciate if anybody could help me with this.

Dani Joseph

alignment
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updated by Biostar Biostar • written by dani357 • dani357

Have you tried BLAT? Does the BAC sequence otherwise look reasonable i.e. it maps to the right genome etc.

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written by GenoMax GenoMax

I haven't tried BLAT. I will try BLAT. My sequences otherwise reasonable. I tried to assemble with canu. But I got repeat the same sequence at another position. So I need to get the vector sequences cut out before assembling. Thank you.

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written by dani357 • dani357

@dani357 Did you ever find a solution?

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written by Bmusungu • Bmusungu

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