Github ltr_retriever

Author: amfe

August undefined, 2024

WebMay 28, 2024 · mcsimenc commented on May 28, 2024. ~50% of the input elements ended up in the *defalse file. ~3% input elements are in the *pass.list files. the *fa files are empty. WebJul 18, 2024 · The whole LTR_retriever pipeline on single computer node is too slow for large genome, so I want to run some steps parallelizing. But I found that I can not get Alignment regions when I run LTR.identifier.pl independently, do you know why? Here are datas and command line I used, all Alignment regions in test.defalse are 0, 0, 0, 0

LTRharvest: Run LTRharvest to predict putative LTR …

WebMay 17, 2024 · RepeatMasker is expecting the search engine NCBI/RMBLAST [ 2.2.27+ ], however, the 2.2.28 version seems to be given to the program. (/home/icar/ncbi-rmblastn-2.2.28-src/c++/GCC480-Debug64/bin/rmblastn). Please double check if the same version of BLAST+ and rmblast is installed. WebLTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences. The Program first constructs all exact match pairs by a suffix-array based algorithm and extends them to … gb4943.1 和訳

questions about solo LTR · Issue #99 · oushujun/LTR_retriever - GitHub

WebLTR_retriever is a command line program (in Perl) for accurate identification of LTR retrotransposons (LTR-RTs) from outputs of LTRharvest, LTR_FINDER, MGEScan 3.0.0, LTR_STRUC, and LtrDetector, and generates non-redundant LTR … Webraw.githubusercontent.com gb495-2002

GitHub - xzhub/LTR_Finder: LTR_Finder is an efficient …

conda install errors · Issue #151 · oushujun/LTR_retriever · GitHub

WebLTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. Long terminal repeat retrotransposons (LTR-RTs) are … WebLTR_retriever An error occurred while fetching folder content. L LTR_retriever Project ID: 3940 Star 0 1 Commit 1 Branch 0 Tags 2.7 MB Project Storage master LTR_retriever … gb4968WebJul 11, 2024 · Hi Shujun, I assembly a 335M diploid plant genome by Falcon-Unzip with 100x PacBio Sequel data, contig N50 9M. After using HiC data, I get chromosome-scale length genome with scaffold N50 32M. I use LTR_retiever to find the LTR in this genome,41.19% of genome are LTR sequence，but the LAI is just 5.22 for this assembly. gb4956-85

"WebNov 11, 2024 · LTR_retriever v2.9.0 ##### Contributors: Shujun Ou, Ning Jiang For LTR_retriever, please cite: Ou S and Jiang N (2024). LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. Plant Physiol. 176(2): 1410-1422. For LAI, please cite: Ou S, Chen J, Jiang N (2024). " - Github ltr_retriever

Github ltr_retriever

Sequence ID length problem · Issue #16 · oushujun/LTR_retriever - GitHub

WebMay 4, 2024 · ERROR: Fail to convert seq IDs to less than 15 character · Issue #14 · oushujun/LTR_retriever · GitHub oushujun / LTR_retriever Public Notifications Fork 36 Star 146 Code Issues 14 Pull requests 1 Actions Projects Security Insights New issue ERROR: Fail to convert seq IDs to less than 15 character #14 Closed WebJun 7, 2024 · LTR_FINDER_parallel and salvage mode · Issue #95 · oushujun/LTR_retriever · GitHub Dear Shujun, I seek your help with understanding how exactly to use salvage mode of your LTR_FINDER_parallel, and also how to avoid using the salvage mode itself, if possible. Before my questions, some context. Generic syntax I am …

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WebApr 22, 2024 · LTRharvest can be used as independently or as initial pre-computation step to sufficiently detect LTR retrotransposons with LTRdigest . Value The LTRharvest … Webuse command below to run LTR Retriever example script for running on Talapas in code folder ([[kimltrret.sh]]) need to make sure that ug has rwx permissions for the …

WebAug 20, 2024 · CST LTR_retriever is starting from the Init step. CST Start to convert inputs... Total candidates: 12800 Total uniq candidates: 12800 CST Module 1: Start to clean up candidates... Sequences with 10 missing bp or 0.8 missing data rate will be discarded. Sequences containing tandem repeats will be discarded. WebJun 1, 2024 · Though it is not directly related to the LTR_retriever, could you kindly help to figure out how to use LTR_retriever data for calculating Copia, Gypsy, and unknown for sliding windows of 50 kb with 25 kb step size. ... Regards, Prabhu, S — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#94 ...

WebJan 31, 2024 · 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. genome-annotation genome-assembly ltr-retrotransposons lai ltr-retriever Updated Jan 31, 2024 Perl oushujun / LTR_FINDER_parallel Star 34 Code Issues WebOct 27, 2024 · EDTA and LTR insertion time · Issue #233 · oushujun/EDTA · GitHub oushujun / EDTA Public Notifications Fork 55 Star 231 Code Issues 46 Pull requests Actions Projects Wiki Security Insights New issue EDTA and LTR insertion time #233 Closed setri100 opened this issue on Oct 27, 2024 · 4 comments setri100 commented on Oct …

LTR_retriever is a command line program (in Perl) for accurate identification of LTR retrotransposons (LTR-RTs) from outputs of LTRharvest, LTR_FINDER, MGEScan 3.0.0, LTR_STRUC, and LtrDetector, and generates non-redundant LTR-RT library for genome annotations. By default, the program will generate whole … See more LTR_retriever is installation-free but requires dependencies: TRF, BLAST+, BLAST or CD-HIT, HMMER, and RepeatMasker. You … See more Two types of inputs are required for LTR_retriever 1. Genomic sequence 2. LTR-RT candidates LTR_retriever takes multiple LTR-RT candidate inputs including the screen … See more Best practice: It's highly recommended to use short and simple sequence names. For example, use letters, numbers, and _ to generate unique names shorter than 15 bits. If there are long … See more The output of LTR_retriever includes: 1. Intact LTR-RTs with coordinate and structural information 1.1. Summary tables (.pass.list) 1.2. GFF3 format output (.pass.list.gff3) 2. … See more

WebMay 31, 2024 · LTR_retriever v1.8.0 ##### Contributors: Shujun Ou, Ning Jiang. Please cite: Ou S, Jiang N: LTR_retriever: a highly accurate and sensitive program for identification of long terminal repeat retrotransposons. Plant Physiology 2024, 176:1410-1422 auton korjauskynäWebSome drug abuse treatments are a month long, but many can last weeks longer. Some drug abuse rehabs can last six months or longer. At Your First Step, we can help you to find 1 … gb4959Webthe docker Image doesn't have complete installation for one of the dependent software, such as RepeatMasker. some of the genome has Long fasta seq name... for unknown reason the LTR-retriever and LAI crashed. gb4962-85WebFeb 7, 2024 · LTR_retriever/bin/Age_est.pl Go to file Cannot retrieve contributors at this time 155 lines (134 sloc) 5.37 KB Raw Blame #!/usr/bin/env perl use warnings; use strict; use File::Basename; my $usage = " Estimate the mean identity of LTR regions in the genome via all-versus-all BLAST gb4950WebFeb 21, 2024 · LTR_retriever 不是一个独立的工具，他的主要作用就是整合 LTRharvest, LTR_FINDER, MGEScan 3.0.0, LTR_STRUC, 和 LtrDetector的结果，过滤其中的假阳 … gb4968-85WebMar 11, 2024 · "Installing" git-filter-repo using Docker. git-filter-repo isn't built-in to git itself. In fact, it's a single Python file, but it's written to feel like a git plugin. And the really nice … auton korjausmaalitWebJun 24, 2024 · questions about solo LTR · Issue #99 · oushujun/LTR_retriever · GitHub oushujun / LTR_retriever Public Notifications Fork 36 Star 147 Issues 10 Pull requests 1 Actions Projects Security Insights New issue questions about solo LTR #99 Closed xiaoyezao opened this issue on Jun 24, 2024 · 5 comments xiaoyezao commented on … gb4982