跟着Plos Genetics学数据分析：LTRpred流程注释完整的LTR（2）运行示例数据

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发布于 2024-02-23 18:41:57

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发布于 2024-02-23 18:41:57

文章被收录于专栏：小明的数据分析笔记本小明的数据分析笔记本

论文

Transposon dynamics in the emerging oilseed crop Thlaspi arvense

https://doi.org/10.1371/journal.pgen.1008370

论文的内容基本都是在围绕着转座子相关

论文的分析代码 https://github.com/acontrerasg/Tarvense_transposon_dynamics

这个R包对应的论文

LTRpred: de novo annotation of intact retrotransposons

github主页 https://github.com/HajkD/LTRpred

帮助文档 https://hajkd.github.io/LTRpred/articles/Introduction.html

今天的推文运行一下这个R包自带的示例数据

运行示例数据的代码

library(LTRpred)
LTRpred(genome.file = system.file("Hsapiens_ChrY.fa", package = "LTRpred"),cores = 24)

参数genome.file 直接提供一个需要分析的基因组的路径

运行这个命令在Step 6有时候会遇到报错，但有时候又没有问题，暂时不知道是啥原因

LTRpred - Step 6:
Starting retrotransposon evolutionary age estimation by comparing the 3' and 5' LTRs using the molecular evolution model 'K80' and the mutation rate '1.3e-07' (please make sure the mutation rate can be assumed for your species of interest!) for 24 predicted elements ...


Please be aware that evolutionary age estimation based on 3' and 5' LTR comparisons are only very rough time estimates and don't take reverse-transcription mediated retrotransposon recombination between family members of retroelements into account! Please consult Sanchez et al., 2017 Nature Communications and Drost & Sanchez, 2019 Genome Biology and Evolution for more details on retrotransposon recombination.

这个步骤是估计逆转录转座子的进化年龄，可以单独运行函数 ltr_age_estimation

LTRpred(genome.file = system.file("Hsapiens_ChrY.fa", package = "LTRpred"),cores = 24,ltr_age_estimation=FALSE)

LTRpred 在运行这个函数的时候增加ltr_age_estimation=FALSE参数跳过step6，然后单独运行函数 ltr_age_estimation

ltr_pred<-read.ltrpred("Hsapiens_ChrY_ltrpred/Hsapiens_ChrY_LTRpred_DataSheet.tsv")
ltr_seqs_3_prime <- "Hsapiens_ChrY_ltrdigest/Hsapiens_ChrY-ltrdigest_3ltr.fas"
ltr_seqs_5_prime<-"Hsapiens_ChrY_ltrdigest/Hsapiens_ChrY-ltrdigest_5ltr.fas"

Hsapiens_ltr_age <- LTRpred::ltr_age_estimation(ltr_pred, ltr_seqs_3_prime, ltr_seqs_5_prime)
Hsapiens_ltr_age