Reference files for TE analysis (v1.1)

README - Transposable Element Differential Expression Analysis Protocol from RNA-seq Data###########################Supplied reference files- Reference genome sequence, predicted RNA sequences and genome annotations (GCA_014300015.1; 2020 genome) These files are publicly available at: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA599375/ GCA_014300015.1_MPIA_NFZ_2.0_genomic.fna GCA_014300015.1_MPIA_NFZ_2.0_genomic.gtf GCA_014300015.1_MPIA_NFZ_2.0_rna_from_genomic.fna- FishTEDB sequences for N. furzeri transposons This file can be obtained at: http://www.fishtedb.org/project/species-detail?species=Nothobranchius+furzeriNothobranchius_furzeri_FishTEDB_TEs.fa- Modified reference files including TE sequences/annotations for* kallisto/transcriptome based method:GCA_014300015.1_MPIA_NFZ_2.0_rna_from_genomic_WithFishTEDBv4.fasta* STAR/genome based method:GCA_014300015.1_MPIA_NFZ_2.0_genomic.fna.maskedGCA_014300015.1_MPIA_NFZ_2.0_gene_and_RepeatMasker_FishTEDB_annotations.gtfGCA_014300015.1_MPIA_NFZ_2.0_genomic.fna.outREADME - 基于RNA-seq数据的转座子（Transposable Element, TE）差异表达分析流程 ########################################################################### ## 提供的参考文件 - 参考基因组序列、预测RNA序列及基因组注释文件（登录号GCA_014300015.1；2020版基因组），此类文件可公开获取于：https://www.ncbi.nlm.nih.gov/bioproject/PRJNA599375/，具体文件包括： GCA_014300015.1_MPIA_NFZ_2.0_genomic.fna GCA_014300015.1_MPIA_NFZ_2.0_genomic.gtf GCA_014300015.1_MPIA_NFZ_2.0_rna_from_genomic.fna - 针对努氏鳉（Nothobranchius furzeri, 简称N. furzeri）转座子的FishTEDB序列文件，获取地址为：http://www.fishtedb.org/project/species-detail?species=Nothobranchius+furzeri，文件名为：Nothobranchius_furzeri_FishTEDB_TEs.fa - 包含转座子序列与注释的修改版参考文件，适配以下两类分析方法： 1. 基于转录组的kallisto分析方法：对应文件为 GCA_014300015.1_MPIA_NFZ_2.0_rna_from_genomic_WithFishTEDBv4.fasta 2. 基于基因组的STAR分析方法：对应文件包括： GCA_014300015.1_MPIA_NFZ_2.0_genomic.fna.masked GCA_014300015.1_MPIA_NFZ_2.0_gene_and_RepeatMasker_FishTEDB_annotations.gtf GCA_014300015.1_MPIA_NFZ_2.0_genomic.fna.out