BLAST unmapped reads from BAM

Question

[ummamd]

Hey, I have sequenced a recombinant plasmid and I am trying to characterize the insert sequences that have not aligned to the reference. I have generated a BAM file with the unmapped sequences and now I am trying to BLAST these in various databases to identify the unmapped sequences.

[JC]

What is your question?

[tomas4482]

Assuming you are studying microbes. Maybe you can try de novo assembly and blast the contig to NCBI or other public database.

Velvet assembler source code: https://github.com/dzerbino/velvet