search

wdecoster / NanoPlot

Plotting scripts for long read sequencing data
http://nanoplot.bioinf.be
MIT License
413 stars 47 forks source link

would Nanoplot support plotting results for a single contig? #379

Closed zhengzhenxian closed 1 month ago

zhengzhenxian commented 1 month ago

@wdecoster

Thanks for developing this great tool!

I am wondering if Nanoplot supports plotting results for a single contig. Occasionally, I have a WGS BAM file but would prefer to obtain statistical results solely for CHR1 to gather basic statistics. This capability would expedite my analysis workflow. Would be great if there is an option for this. Thank you very much.

Zhenxian

wdecoster commented 1 month ago

Hi Zhenxian,

No, that is currently not supported. One solution would be to use cramino, while reading from stdin. If you only care about statistics then you are done. If you want a plot you could use the arrow file.

Something like:

samtools view alignment.bam chr1 | cramino --arrow data.arrow > statistics.cramino
NanoPlot --arrow data.arrow <etc>

Best, Wouter

zhengzhenxian commented 1 month ago

Cool, I will try cramino then!