This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Difficult using Nanoplot

Hello all,

I am using NanoPlot for generating the plot form ONT data. I am using the following command:

NanoPlot --bam trim.sort.bam -o /path/out/

The input bam file is ~1GB

I have started running the command for more than two hours. Is it normal for nanplot to take that long?or am I missing something?

TIA

nanoplot ont
• 3,309 views • link
written by KVC_bioinfo KVC_bioinfo

Could you share the log file? It's in the output directory you specified. It contains timestamps per step so we can check what's the slow part.

For sure the kernel density estimate plots (kde) are quite slow on big datasets. You can specify which plotting styles you want using the --plots argument.

Also, which organism are you working on? For feature extraction NanoPlot parallelizes per chromosome.

(it makes probably more sense to provide a link to the github repository rather than to my blog, although it's nice to attract some traffic)

• 0 views • link
written by WouterDeCoster WouterDeCoster

Thanks! It just stopped after 2:30 hours and gave results. Worked very fine. Thanks.

• 0 views • link
written by KVC_bioinfo KVC_bioinfo

Good to hear. Nevertheless, that's quite long. Would you mind sharing the log file?

Always interested in suggestions or feature requests!

• 0 views • link
written by WouterDeCoster WouterDeCoster

I will share it. Shall I email?

• 0 views • link
written by KVC_bioinfo KVC_bioinfo

That's okay,

decosterwouter AT gmail DOT com

• 0 views • link
written by WouterDeCoster WouterDeCoster

0 answers

No answers yet.

Log in to answer this question.

More posts like this