How to split alignment into smaller chunks with node range

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3 months ago

Wenhai • 0

Hi,

I have a GFA file(graph) and GAM file(alignment). I want to split them into smaller chunks with node range. I have splited GFA file into smaller chunks with command vg chunk -r 1527845:2392738 -x test.gfa -O gfa > chunk303.gfa, but I got an error when I splited GAM file with command vg chunk -a gfa_mapped_sort.gam -r 1527845:2392738 > chunk303_mapped.gam.

I don't know whether my command is right or not.

Thank you in advance!

vg • 301 views

ADD COMMENT • link updated 3 months ago by Jordan M Eizenga ▴ 460 • written 3 months ago by Wenhai • 0

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Can you be more specific about the error that you encountered? Was there any output to stderr? I think the error might be that your GAM was saved to a file in your working directory rather than emitted through stdout. Did you check the working directory?

ADD REPLY • link 3 months ago by Jordan M Eizenga ▴ 460

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