How to find the co ordinates of long reads (simulated by Badreads) with respect to the reference genome
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10 weeks ago
Ashi ▴ 10

Hi,

I have simulated a set of ONT long reads (10x) of E coli using the Badreads simulator tool. I was wondering is there any way I can know the co ordinates (positions) of these long reads in the reference genome. I know most simulators have some metadata attached to the files that they are generating, but I could not find any thing like that in the Badreads file.

Does any one have any idea?

Thank you for all the help.

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You can use minimap2 to align the reads back to the genome and identify starting coordinates that way.