How to find the co ordinates of long reads (simulated by Badreads) with respect to the reference genome

0

Entering edit mode

3.3 years ago

Ashi ▴ 20

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?

Badread Tool github page : https://github.com/rrwick/Badread

Thank you for all the help.

long-reads reference-genome assembly • 735 views

ADD COMMENT • link updated 7 months ago by Ram 44k • written 3.3 years ago by Ashi ▴ 20

0

Entering edit mode

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

ADD REPLY • link 3.3 years ago by GenoMax 147k

Login before adding your answer.