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
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