Draw Repeat Landscapes

[CraigMichell]

Hi,

This is not a complaint about the program at all. I think that it is great and easy to use. I have been able to identify repeat elements in two genomes now with relative ease. I am a relative newbie to the area of repeat genomics and I would like to continue the analysis with the repeats identified from the EDTA pipeline.

Would you be able to advise on the best way to use the information from EDTA to create a repeat landscape type plot? I tried taking the repeat library created and masking my genome using that with RepeatMasker and following the next few steps for creating a repeat landscape plot. But the landscape plot is empty, I have a feeling it is because the classification of repeats is different? But as I said, I am a bit naive when it comes to analysis of repeat elements.

Any help or suggestions would be greatly appreciated. Thanks!

[oushujun]

Hello,

Thank you for using EDTA. There are many ways you can approach your goal, but most, if not all, of them, require some coding skills in one kind or the other. I have an old code that was developed to summarize LTR density in the LTR_retriever package: https://github.com/oushujun/LTR_retriever/blob/master/bin/LTR_sum.pl.

Alternatively, you may try karyoploteR, which is made to fulfill similar tasks. But again, this time you need some R coding skills. Similarly, you can also try a simpler version in ggplot: https://www.biostars.org/p/69748/

Hope these are helpful and feel free to share your codes here.

Best, Shujun

[KristinaGagalova]

I don't know if you figured that out but I've made my own visualization with R using the results from RepeatMakser - createRepeatLandscape.pl + the histogram information at the bottom of the output file. You can create a stacked barplot with ggplot2 which works perfectly for a publication. Let me know if you still need hep with that!

[oushujun]

@KristinaGagalova Can you share the codes and usage here so that other uses may benefit from your hard work? Thanks!

[KristinaGagalova]

Yes, of course! Should I just upload my script here with some examples data or anywere you like better?

[oushujun]

@KristinaGagalova Please upload them here. I have pinned this issue to the top so that everyone looking for this kind of illustration will see it. Thanks Kristina!

[KristinaGagalova]

Code is below

#############################
###Plot Kimura distance######
#############################

library(reshape)
library(ggplot2)
library(viridis)
library(hrbrthemes)
library(tidyverse)
library(gridExtra)

sessionInfo()
#R version 3.6.1 (2019-07-05)
#Platform: x86_64-conda_cos6-linux-gnu (64-bit)
#Running under: Ubuntu 20.04.1 LTS

#attached base packages:
#  [1] stats     graphics  grDevices utils     datasets  methods   base     
#other attached packages:
#  [1] gridExtra_2.3     forcats_0.5.0     stringr_1.4.0     dplyr_0.8.5       purrr_0.3.4      
#  [6] readr_1.3.1       tidyr_1.1.0       tibble_3.0.1      tidyverse_1.3.0   hrbrthemes_0.8.0 
#  [11] viridis_0.5.1     viridisLite_0.3.0 ggplot2_3.3.0     reshape_0.8.8    

KimuraDistance <- read.csv("/path/to/the/tbl/file",sep=" ")

#add here the genome size in bp
genomes_size=230000000

kd_melt = melt(KimuraDistance,id="Div")
kd_melt$norm = kd_melt$value/genomes_size * 100

ggplot(kd_melt, aes(fill=variable, y=norm, x=Div)) + 
  geom_bar(position="stack", stat="identity",color="black") +
  scale_fill_viridis(discrete = T) +
  theme_classic() +
  xlab("Kimura substitution level") +
  ylab("Percent of the genome") + 
  labs(fill = "") +
  coord_cartesian(xlim = c(0, 55)) +
  theme(axis.text=element_text(size=11),axis.title =element_text(size=12))

Below a the expected input (generated by createRepeatLandscape.pl from RepeatMasker) Test_createRepeatLandscapePlot.txt

Expected output

This plots all the classes of repeats, we may want to create a more efficient grouping of those, using the output from EDTA and including that into few classes of repeats.

[oushujun]

@KristinaGagalova Thanks for sharing the code. I notice that Gypsy is missing the input and the figure, is it something wrong or you want to leave it out?

[KristinaGagalova]

@oushujun Just for double checking, below the summary from EDTA

Repeat Classes
==============
Total Sequences: 5497
Total Length: 201821862 bp
Class                  Count        bpMasked    %masked
=====                  =====        ========     =======
DNA                    --           --           --   
    DTA                10262        2182169      1.08% 
    DTC                15205        3015590      1.49% 
    DTH                4129         831309       0.41% 
    DTM                24634        5549959      2.75% 
    DTT                2161         400460       0.20% 
    Helitron           16470        3333789      1.65% 
LTR                    --           --           --   
    Copia              23           7180         0.00% 
    unknown            6364         1346226      0.67% 
MITE                   --           --           --   
    DTA                1946         352337       0.17% 
    DTC                353          73131        0.04% 
    DTH                315          60310        0.03% 
    DTM                1804         297687       0.15% 
    DTT                4            448          0.00% 
                      ---------------------------------
    total interspersed 83670        17450595     8.65%

---------------------------------------------------------
Total                  83670        17450595     8.65%

Looks like the pipelinen did not identify any of LTR Gypsy, I am not sure if that's unusual. I have also added the repeats from Repbase from a closer species that has several LTR but looks like RepeatMasker did not identify also those This is hower a small genomes and with low % of repeats. If you have any feedback on that may be helpful, but the image reflects the repeats annotation.

[oushujun]

@KristinaGagalova I see, that makes sense! Thanks for sharing your data and the code.

[aaronphillips7493]

Hello,

I am interested in producing a similar plot for my genome of interest. I have recently run EDTA on the genome. Is the Kimura substitution plot possible to make from the output of EDTA (i.e. is the output in one of the RepeatMasker directories)? r do I need to run RepeatMasker separately using the TE library generated by EDTA?

Thank you in advance, Aaron :)

[oushujun]

Hi Aaron,

If you check the above conversations, you will see the input is obtained from createRepeatLandscape.pl from RepeatMasker. While I never tried myself, you may check it out and see what the script needs.

Best, Shujun

On Fri, Feb 26, 2021 at 12:20 PM aaronphillips7493 notifications@github.com wrote:

Hello,

I am interested in producing a similar plot for my genome of interest. I have recently run EDTA on the genome. Is the Kimura substitution plot possible to make from the output of EDTA (i.e. is the output in one of the RepeatMasker directories)? r do I need to run RepeatMasker separately using the TE library generated by EDTA?

Thank you in advance, Aaron :)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/92#issuecomment-786400960, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NCE6GX4WEZRDOB53F3TA4ORHANCNFSM4OTDDQUA .

[aaronphillips7493]

Hey Shujun,

Thank you for your reply. I apologise, I got confused by the "RM" files generated by EDTA. I forgot that they come from Repeat Modeller not Repeat Masker. It seems I will have to run Repeat Masker separately and then follow createRepeatLandscape.pl from RepeatMasker.

Aaron :)

[oushujun]

Sorry this is confusing. RM could be both in different context. It means RepeatModeler in the final folder and RepeatMasker in all other contexts. So you can get a masker-like out file in the anno folder, but I am not sure if RepeatMasker can recognize it. -Shujun

On Fri, Feb 26, 2021 at 2:24 PM aaronphillips7493 notifications@github.com wrote:

Hey Shujun,

Thank you for your reply. I apologise, I got confused by the "RM" files generated by EDTA. I forgot that they come from Repeat Modeller not Repeat Masker. It seems I will have to run Repeat Masker separately and then follow createRepeatLandscape.pl from RepeatMasker.

Aaron :)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/92#issuecomment-786440931, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NG7FT7I55WLYT3R3BLTA45BPANCNFSM4OTDDQUA .

[CraigMichell]

Now that I have finally been able to come back to analysing the repeats almost a year later. I just wanted to thank everyone for their suggestions and help with this.

I thought I would outline the commands that I used in the end for generating a repeat landscape from the EDTA library.

• singularity_wrapper exec EDTA.pl --genome genome.fasta --species others --step all --anno 1 --threads 16 --overwrite 1
• RepeatMasker -pa 2 -s -a -inv -dir ./RepMask -no_is -norna -xsmall -nolow -div 40 -lib EDTA.TElib.fa -cutoff 225 genome.fasta
• calcDivergenceFromAlign.pl -s genome.divsum genome.fasta.align

The Kimura distance table is made up of the last 72 lines of the divsum file and can be extracted using

• tail -n 72 genome.divsum > genome.Kimura.distance

This then provides table which can be read into the R script from @KristinaGagalova above.

A compilation of the landscapes that I plotted are attached.

I am interested in figuring out what is up with the large peak with a Kimura distance of 0 in each of the landscapes. Could it be some artifact of the process?

[oushujun]

Thanks for sharing your route! You may want to check the LTR Assembly Index to make sure these genomes are in good Quality for fair comparison. It seems to me that the lappo genome has higher quality than the aestiva genome.

-Shujun

On Fri, May 28, 2021 at 6:51 PM CraigMichell @.***> wrote:

Now that I have finally been able to come back to analysing the repeats almost a year later. I just wanted to thank everyone for their suggestions and help with this.

I thought I would outline the commands that I used in the end for generating a repeat landscape from the EDTA library.

• singularity_wrapper exec EDTA.pl --genome genome.fasta --species others --step all --anno 1 --threads 16 --overwrite 1
• RepeatMasker -pa 2 -s -a -inv -dir ./RepMask -no_is -norna -xsmall -nolow -div 40 -lib EDTA.TElib.fa -cutoff 225 genome.fasta
• calcDivergenceFromAlign.pl -s genome.divsum genome.fasta.align

The Kimura distance table is made up of the last 72 lines of the divsum file and can be extracted using

• tail -n 72 genome.divsum > genome.Kimura.distance

This then provides table which can be read into the R script from @KristinaGagalova https://github.com/KristinaGagalova above.

A compilation of the landscapes that I plotted are attached.

[image: Repeat_Landscapes] https://user-images.githubusercontent.com/39945819/119971780-1578e980-bfba-11eb-8148-17308e076cfc.jpg

I am interested in figuring out what is up with the large peak with a Kimura distance of 0 in each of the landscapes. Could it be some artifact of the process?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/92#issuecomment-850332587, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4ND67MAOSJIMU6UDMP3TP5YT7ANCNFSM4OTDDQUA .

[KristinaGagalova]

This looks like an interesting package - https://github.com/dwinter/repeatR

[BenAawf]

First of all, thank you all. I would appreciate it if any could help me understand what those values (numbers) mean in simple words : Div DNA/DTA DNA/DTC DNA/DTH DNA/DTM DNA/DTT DNA/Helitron LTR/Copia LTR/unknown MITE/DTA MITE/DTC MITE/DTH MITE/DTM MITE/DTT Simple_repeat 0 56501 195150 74881 366703 31760 265453 1597 8915 15679 6790 3767 19197 448 0 1 4129 18025 1400 25603 1085 26781 0 55 999 251 70 10725 0 0 2 7610 30725 3424 32479 761 18890 0 2067 3992 154 87 9642 0 0 3 13590 51664 6968 50551 1026 25304 627 1250 6389 1838 125 9066 0 0 4 21745 57150 10975 64491 3487 35745 1091 3717 11783 2957 310 9757 0 0 5 35444 65082 17207 80812 2897 48271 770 5976 13448 2987 840 10382 0 0

the above data is a head file from @KristinaGagalova dataset

Thank you

[KristinaGagalova]

Hi, these are the type of repeats that are annotated (broad definition) and their corresponding counts in the genome. It's basically a quantification per class. The div column shows the % divergence and it's the x-axis in Kimura plot

[joannarifkin]

https://github.com/jtlovell/GENESPACE might be helpful here too!

[oushujun]

By default now EDTA (v2.2.1) will draw the repeat landscape directly as one output. Here's what it looks like:

I am unpinning this thread for its retirement. Thank you everyone for providing codes and ideas for this topic!!

Shujun

[ltswx]

@KristinaGagalova

Thanks for sharing！ but I'm confused ，I added up all the numbers in the divsum file except for the first column and divided by the size of the genome,；There is a huge difference between the results of the two, the result of the *EDTA file is 68.17%, and the result of my calculation is 98%！, I would like to ask where I misunderstood，Because I'm trying to draw a pie chart that shows the percentage of these transposons QAQ

*mod.EDTA.TEanno.sum： Repeat Classes

Total Sequences: 3487 Total Length: 1322312127 bp Class Count bpMasked %masked ===== ===== ======== ======= LTR -- -- --
Copia 105891 108126703 8.18% Gypsy 292804 391191137 29.58% unknown 182543 139936847 10.58% TIR -- -- --
CACTA 61380 26705216 2.02% Mutator 107653 114277135 8.64% PIF_Harbinger 28574 8112964 0.61% Tc1_Mariner 125476 35791242 2.71% hAT 46252 20984760 1.59% nonTIR -- -- --
helitron 148352 56359955 4.26%

total interspersed 1098925      901485959    68.17%

---

Total 1098925 901485959 68.17% —————————————————————————— tbl file form repeatmasker: total length: 1333551035 bp (1322312127 bp excl N/X-runs) GC level: 36.87 % bases masked: 946989405 bp ( 71.01 %) —————————————————————————— divsum file: Div DNA/DTA DNA/DTC DNA/DTH DNA/DTM DNA/DTT DNA/Helitron LTR/Copia LTR/Gypsy LTR/unknown MITE/DTA MITE/DTC MITE/DTH MITE/DTM MITE/DTT 0 2372488 1566743 448260 1399704 1862233 3080962 4090922 14477189 2989812 125802 12497 41037 54060 84787 1 1070198 565642 179819 699623 1098895 2032132 2420914 10119770 2200132 10879 422 4182 3855 8880 2 715860 855177 218688 527116 470136 824655 1995255 11309963 2177667 10787 217 13666 6496 22494 3 1035157 842382 208109 521912 349325 986025 3128677 13492012 2677114 34770 2122 23326 24197 34870 4 781227 794300 166625 727909 508392 1212696 5397677 12978613 3680115 38307 642 28485 42707 45816 5 1406210 769048 173994 906731 624432 1341063 4343808 15285779 4647044 52326 0 27940 63166 54184 6 770654 831030 197007 713560 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