ambika Pokhrel - 2021-05-19

Hello everyone,

I am following one paper https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2486-8 in order to distinguish the core and accessory chromosomes of several genomes that I am working with. For this I did PROmer alignment, and generated the output files (delta and coords files). From the paper they say that the scaffolds with >=30% of their length covered by unique promer matches to core chromosomes of reference genome were considered core chromosomes and the rest as accessory chromosome.
The codes that I used are as below:

promer --mum --prefix=Nechacore-T2 77-13-4_masked_core.fasta T2_AssemblyScaffolds_Repeatmasked.fasta
delta-filter -g Nechacore-T2.delta > Nechacore-T2-filtered.delta
show-coords -rcl Nechacore-T2-filtered.delta > Nechacore-T2.coords

The output that I am getting now (coords file) looks like this:

   [S1]     [E1]  |     [S2]     [E2]  |  [LEN 1]  [LEN 2]  |  [% IDY]  |  [LEN R]  [LEN Q]  |  [COV R]  [COV Q]  | [TAGS]
===============================================================================================================================
       1     2549  |  2206083  2203513  |     2549     2571  |    94.37  |  6854980  2629525  |     0.04     0.10  | NC_030986.1        scaffold_12
    2548     4559  |    46756    48770  |     2012     2015  |    96.23  |  6854980  6421299  |     0.03     0.03  | NC_030986.1        scaffold_1
    5106     5803  |  2200059  2199362  |      698      698  |    97.56  |  6854980  2629525  |     0.01     0.03  | NC_030986.1        scaffold_12
    5951     8504  |  2199309  2196748  |     2554     2562  |    98.20  |  6854980  2629525  |     0.04     0.10  | NC_030986.1        scaffold_12
   45565    48326  |    49371    52160  |     2762     2790  |    96.06  |  6854980  6421299  |     0.04     0.04  | NC_030986.1        scaffold_1

What I do not understand is how to calculate the coverage of each scaffold from this data and set the cutoffs as >=30% to define the core chromosomes. Please help!!

Thanks
AP