Question: Reads length Distribution of ONT reads and Error rate
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gravatar for midox
23 months ago by
midox210
Tunisia
midox210 wrote:

Hello,

I want to know the distribution of the reads and the error rate (mismatch, insertion, deletion) of the Nanopore Sequencing Technology.

Thank you

ADD COMMENTlink modified 23 months ago by WouterDeCoster37k • written 23 months ago by midox210
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gravatar for Brian Bushnell
23 months ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

BBMap can report those statistics, though reads longer than 6kbp will be broken into 6kbp segments. For this purpose, that shouldn't matter, though it's worth noting that the shorter the fragments, the lower the apparent error rate is.

mapPacBio.sh in=reads.fastq maxlen=6000 out=mapped.sam ref=reference.fasta

That will report the rates of mismatches, insertions, and deletions.

ADD COMMENTlink written 23 months ago by Brian Bushnell16k

in the case of PacBio reads or i can also use Nanopore?

ADD REPLYlink written 23 months ago by midox210

The error rates of PacBio and Nanopore are similar (both extremely high) so I use the same error profile. Though in practice, Nanopore error rates seem to be much higher than PacBio, so to map as many reads as possible, you can reduce the kmer length and increase sensitivity. But... nobody really cares about reads with under 75% identity, so I'd just classify those as junk, and ignore them.

ADD REPLYlink written 23 months ago by Brian Bushnell16k

I am looking for a distribution that already exists of number of nanopore reads according to their lengths and the different error rates. If I can do it with BBmap I try to map the raw reads on the reference genome and extract this informations.

ADD REPLYlink written 23 months ago by midox210

You can't directly get a distribution of error rates by read length with BBMap with reads over 6kbp, since it chops reads. It's easy to post-process, though, since the chopped reads still contain their name.

ADD REPLYlink written 23 months ago by Brian Bushnell16k

Please brian. When I do mapping sequences on the reference genomes using BBmap I consider the overall mapping rate in "pct bases" ?? Thanks

ADD REPLYlink modified 23 months ago • written 23 months ago by midox210
1

@Brian referred to this recently here.

ADD REPLYlink written 23 months ago by genomax64k

Please brain.

Are you talking to Brian or your brain?

ADD REPLYlink written 23 months ago by WouterDeCoster37k

oups sorry. To Brian. and everyone

ADD REPLYlink written 23 months ago by midox210
0
gravatar for WouterDeCoster
23 months ago by
Belgium
WouterDeCoster37k wrote:

It's impossible to make an accurate statement about the distribution of read lengths, since these are dependent on the length of the input DNA and how careful you treat the library. With the most common library prep you have reads of 6-10kb, with a long tail up to ~200kb.
However, with an adapted protocol, very careful handling and old-school DNA extraction you can get reads of up to 970kb, as reported by Nick Loman and Josh Quick.

ADD COMMENTlink written 23 months ago by WouterDeCoster37k
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