RepeatMasker (会自动安装所以来的TRF和RMblast) 所以偷懒,依次用conda安装了上述软件。 同样用conda安装了LTR_FINDER;按照教程完成了第一步的分析。 但是第二步时(LTR_retriever -threads 4 -genome Athaliana.fa -infinder Athaliana.finder.scn),报错,原因为:Dependency checking: Error: The RMblast engine is ...
cdLTR_FINDER_parallel-1.1perlLTR_FINDER_parallel LTR_FINDER_parallel使用方法: perl LTR_FINDER_parallel -seq ${genome} -threads 36 -harvest_out #输出是${genome}.finder.combine.scn genomefile="`basename ${genome}`" mv ${genomefile}.finder.combine.scn ${species}.finder.scn 当使用conda时候,可...
Quick installation using conda Standard installation Inputs Outputs Usage Citations Introduction 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 ge...
conda install -c bioconda ltr_retriever Step by step using conda You may use conda to quickly install all dependencies and LTR_retriever is then good to go: conda create -n LTR_retriever conda activate LTR_retriever conda install -y -c conda-forge perl perl-text-soundex conda install -y -...
conda install -y -c bioconda cd-hit repeatmasker git clone https://github.com/oushujun/LTR_retriever.git ./LTR_retriever/LTR_retriever -h chmod 757 gt-1.6.2/bin/gt chmod 757 seqkit chmod 757 LTRfind chmod 757 LTR_FINDER_parallel-1.1/bin/LTR_FINDER.x86_64-1.0.7/ltr_finder ./LTRfind...
conda install -c bioconda/label/cf201901 repeatmasker git clone https://github.com/oushujun/LTR_retriever.git ./LTR_retriever/LTR_retriever -h 此外你还需要额外安装LTRharvest,LTR_FINDER和MGEScan_LTR。 LTRharverst:http://genometools.org/
LTR_retriever根据LTR_FINDER的输出识别LTR-RT,生成非冗余LTR-RT文库,可用于基因组注释 /data/pub/liuzy/software/LTR_retriever/LTR_retriever-threads4-genome groups.asm.fasta-infinder groups.asm.finder.scn 这里的-infinder表示输入来自于LTR_FINDER,它支持同时输入LTRharvest的输出(-inharvest)和 MGEScan-LTR...
$conda install -y -c bioconda cd-hit repeatmasker $git clone https://github.com/oushujun/LTR_retriever.git $./LTR_retriever/LTR_retriever -h 除此之外还需要安几个依赖的软件 1.makeblastdb,blastn,andblastxintheBLAST+package(ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)2....
conda install-c bioconda/label/cf201901 repeatmasker git clone https://github.com/oushujun/LTR_retriever.git./LTR_retriever/LTR_retriever-h 此外你还需要额外安装LTRharvest,LTR_FINDER和MGEScan_LTR。 LTRharverst:http://genometools.org/ LTR_FINDER:https://github.com/xzhub/LTR_Finder ...
Quick installation using conda Standard installation Inputs Outputs Usage Citations Introduction 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 ge...