LTR_retriever
LTR_retriever copied to clipboard
oushujun
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
Hi Shujun ! Thinks for you biosoft LTR_retriever, but now I 'am enconter some problem that what means "-0" of Insertion_Time in .pass.list files?
Hi, @oushujun For big genomes, can I split genome to run this pipeline to get the LAI? In this way, it's faster than the whole genome. Best wishes!
Dear shujun， First of all apologize for my bad English. I have sequenced dozens species, these species belong to the same genus (eg. wild, cultivars, landrances), and I will construct...
Hi Dr.Ou, I have got another question about the input of LTR_retriever. You give an example of how to run ltr_harvest and ltr_finder, and I run the two software as...
Dear @oushujun, Thanks for a wonderful tool! I have run this on a very large LTR_FINDER dataset from a large genome and poked around a little in the code. I...
Thank you for your work. LAI did not run correctly.While running I get the following error `$genome.tbl: No such file or directory` After checking I found out that it is...
Hello Shujun Ou： when I run the LTR_retriever, It happened errors as follows: ERROR: RepeatMasker is not running properly! Please check the file Genome.fa.ltrTE.mask.lib and Genome.fa.ltrTE.trunc and test run: RepeatMasker...
Hello Sir I am getting empty output file after using **call_seq_by_list.pl** I used gt suffixerator, gt ltrharvest, ltr_finder, LTR_retriever and awk '{if ($1~/[0-9]+/) print $10"\t"$1}' to get the output_d file....
There may be a bug for the script solo_intact_ratio.pl. The intact LTR count always less 1 than the real count. I fixed it like: #!/usr/bin/perl -w use strict; use 5.010;...
Upon first encountering an ID, the counts for solo and intact are both initialized to zero, failing to count the first occurrence of a solo or intact element for each...
