Github ltr_retriever
WebNov 13, 2024 · oushujun / LTR_retriever Public Notifications Fork 36 Star 146 Actions Projects Insights New issue perl: symbol lookup error #59 Closed wuxiaopei0509 opened this issue on Nov 13, 2024 · 5 comments wuxiaopei0509 commented on Nov 13, 2024 oushujun label on Nov 14, 2024 completed on Nov 25, 2024 to join this conversation on … 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 ...
Github ltr_retriever
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WebFeb 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 WebHi, I got errors when install using conda, do you know why? Best, Kun
WebMar 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 … 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 …
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. 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 …
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 …
WebAug 11, 2024 · CST Dependency checking: All passed! CST LTR_retriever is starting from the Init step. CST Start to convert inputs... Total candidates: 3714 Total uniq candidates: 3279 CST Module 1: Start to clean up candidates... is mitsubishi galant a good carWebLTR_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 … is mitsubushi good for taxiWebLTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package. - LTR_retriever/Dockerfile at master · oushujun/LTR_retriever is mitsubishi still in businessWebJul 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. is mitsuri and obanai canonLTR_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 is mitsubishi mirage good carsWebLTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. Long terminal repeat retrotransposons (LTR-RTs) are … is mitsubishi the best mini splitWebthe 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. is mitsuri better than shinobu