Question: converting fast5 to fasta failed
0
gravatar for Ric
9 months ago by
Ric270
Australia
Ric270 wrote:

I tried to use poretoos to convert fast5 to fasta file but the below command did not create any file

> poretools fasta --type best 15
> poretools fasta --type best 15/*
> poretools fasta --type best 15/*.fast5

What did I miss you?

Thank you in advance,

sequence • 395 views
ADD COMMENTlink modified 9 months ago by Heather Ward50 • written 9 months ago by Ric270
1

How did you obtain these fast5 files? Are those basecalled?

By the way, since the basecallers can output fastq directly poretools is, well, obsolete now.

ADD REPLYlink written 9 months ago by WouterDeCoster40k

We ask sequence company to sequence our genome. Is there any other software available?

ADD REPLYlink written 9 months ago by Ric270

Then you could ask that company what they send you: raw or base called fast5. Or you could share one fast5 file with me/us and I can have a look. In any case, you can do the basecalling yourself, using albacore, which you can get from the nanopore community forum.

ADD REPLYlink written 9 months ago by WouterDeCoster40k
0
gravatar for Heather Ward
9 months ago by
Heather Ward50
Guelph, ON
Heather Ward50 wrote:

It may be that your files don't have the type of reads that best extracts. Have you tried using some of the other types, for example 2D, or no type at all? If that outputs something, it's likely that your file doesn't have any reads that match the type best, which doesn't seem to make much sense -- the poretools documentation seems to imply that something should be output when using best:

A type of “best” will extract the 2D read, if it exists. If not, it will extract either the template or complement read, whichever is available and has a better average Phred score.

Also keep in mind that the fasta file will be output to stdout; if you'd like them in a file, you'll have to redirect the output.

ADD COMMENTlink written 9 months ago by Heather Ward50

I tried all and 2d none of them have created an output.

ADD REPLYlink written 9 months ago by Ric270
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