Question: Remove vector sequences
gravatar for dani357
22 months ago by
dani3570 wrote:

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 • 778 views
ADD COMMENTlink modified 20 months ago by Biostar ♦♦ 20 • written 22 months ago by dani3570

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

ADD REPLYlink written 22 months ago by genomax71k

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.

ADD REPLYlink written 22 months ago by dani3570

@dani357 Did you ever find a solution?

ADD REPLYlink written 18 months ago by Bmusungu20
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