Reference files for analysis of TE transcription in African Turquoise Killifish

README - Transposable Element Differential Expression Analysis Protocol from RNA-seq Data###########################<br>Supplied reference files<br>- 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<br>- FishTEDB sequences for N. furzeri transposons This file can be obtained at: http://www.fishtedb.org/project/species-detail?species=Nothobranchius+furzeri Nothobranchius_furzeri_FishTEDB_TEs.fa<br>- Modified reference files including TE sequences/annotations for * kallisto/transcriptome based method: GCA_014300015.1_MPIA_NFZ_2.0_rna_from_genomic_WithFishTEDBv4.fasta<br> * STAR/genome based method: GCA_014300015.1_MPIA_NFZ_2.0_genomic_WithFishTEDBv4.fasta GCA_014300015.1_MPIA_NFZ_2.0_genomic_WithFishTEDBv4.gtf<br><br>Related to repository: https://github.com/BenayounLaboratory/Killifish_Transposon_Quantification<br>README - 基于RNA-seq数据的转座子（Transposable Element）差异表达分析协议 ### 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（GCA_014300015.1；2020版基因组）。这些文件可公开获取于：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 - 用于假鳃鳉（*Nothobranchius furzeri*）转座子的FishTEDB序列文件，该文件可从以下地址获取：http://www.fishtedb.org/project/species-detail?species=Nothobranchius+furzeri，文件名为：Nothobranchius_furzeri_FishTEDB_TEs.fa - 适配两类分析方法的含转座子序列/注释的修改版参考文件： - 基于kallisto/转录组的分析方法：GCA_014300015.1_MPIA_NFZ_2.0_rna_from_genomic_WithFishTEDBv4.fasta - 基于STAR/基因组的分析方法： GCA_014300015.1_MPIA_NFZ_2.0_genomic_WithFishTEDBv4.fasta GCA_014300015.1_MPIA_NFZ_2.0_genomic_WithFishTEDBv4.gtf 关联仓库地址：https://github.com/BenayounLaboratory/Killifish_Transposon_Quantification