No spectra plots for repeats 9-14 bp in Summary_output when running Setup_Run_Repeats.sh

[chrisjackson-pellicle]

Hi @celphin,

Thanks very much for this software, I've found it very useful!

When running the script Setup_Run_Repeats.sh, I noticed that there is no spectra plot in the Summary_output folder for repeats in the range 9-14 bp. This range is also skipped in the repo documentation for these plots. However, I noticed that there is a specta plot for repeats 5-200 bp in the folder .../output_chromosomes/nep_contig_23_H0-AT/Chr1part01/largeimages.png/All_spec1_nep_contig_23_H0-AT_Chr1part01_bp5_200seq2501_19977501TRUE.png.

For this particular chromosome the dominant repeats are ~9 bp, and hence only appear in this plot:

Can you tell me if this plot (or a plot specifically for repeats 9-14 bp) is omitted deliberately from the Summary_output folder?

Thanks very much,

Chris

[celphin]

Hi Chris,

Sorry for the slow response - I have been away traveling. I'm just looking through these issues now.

There was no reason to specifically exclude 9-14bp. I'm glad you found the 5-200bp spectra. The full spectra (2-1500bp) are included in all the calculations for Shannon diversity etc. For the spectra plots, I found it easier to visualize the patterns on smaller scales so just plotted some repeat lengths in the summary output. Thanks for pointing out that I missed that range of repeat lengths completely though.

You can make your own plots with any range of repeat lengths using the following the code in this link directly in R: https://github.com/celphin/RepeatOBserverV1?tab=readme-ov-file#plotting-a-new-specific-range-of-repeat-lengths-in-the-heatmaps-of-the-fourier-spectra
To run the code in the link above you need to have the directories setup as they are after the program finished running.

Input the follow parameters for your genome/species/chromosome:

inpath="~/scratch/repeats/input_chromosomes/Fly/chromosome_files/"
fname= "Fly_H0"
chromosome="ChrDlow77"
part="part01"
nam="Fly_H0_ChrDlow77part01"

Copy and paste the rest of the code as is from the link above updating only the range of bp that you want. Currently set to 17-30 bp.
r1=base::c(17,30)

Please let me know if you run into any problems and I'm happy to try to answer questions.