Question: Including failed minION reads in alignment
0
gravatar for eayasi
2.2 years ago by
eayasi0
eayasi0 wrote:

I am trying to get data from a minION run I have done. Most of my reads a pretty low quality (rapid seq kit with shortened fragmentation on 8kb plasmid...might be the problem?) and over half failed. enter image description here I've tried to use a few aligners like bwa-mem, graphmap, last - but nothing is aligning to my plasmid. Is it worth it to to try the failed reads? Will I get usable/ok data with enough coverage?

Is there a way to extract fastq/a files from just the failed reads using poretools or nanoOK? Any tips would be appreciated!

minion alignment • 1.0k views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by eayasi0

If nothing is aligning, you might try BLAST on a few hundred reads (or, in fact, BBSketch on all of them) to see if you have contamination. Is this plasmid likely to be on NCBI (RefSeq/nt)?

I'm not sure what "failed" means to Nanopore software, but it's likely that you can't extract them as fasta/fastq because the bases simply have not been called. You can't align the raw signal.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Brian Bushnell16k

Thanks for your reply. I have had one read align in graphmap. :/ I have blasted some and gotten yeast mitochondrial DNA (makes sense since I isolated plasmid from yeast). Might have to rethink seq protocol to get usable data.

ADD REPLYlink written 2.2 years ago by eayasi0

Did you use bwa-mem -x ont2d?

The majority of your reads are also rather short, it seems.

ADD REPLYlink written 2.2 years ago by WouterDeCoster40k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1180 users visited in the last hour