Remove vector sequences

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7.0 years ago

dani357 ▴ 10

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 • 2.0k views

ADD COMMENT • link updated 6.9 years ago by Biostar 20 • written 7.0 years ago by dani357 ▴ 10

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

ADD REPLY • link 7.0 years ago by GenoMax 147k

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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.