├── .gitignore ├── Dockerfile ├── ExampleData ├── testData_human.fastq.err ├── testData_human.fastq.gz ├── testData_human.fastq.log ├── testData_human.fastq.qcResult ├── testData_human.fastq.stats ├── testData_human.fastq │ ├── Progress_1_FoundAdapter.dat │ ├── endogenousAlignments_Accepted.dict │ ├── endogenousAlignments_Accepted.txt.gz │ ├── endogenousAlignments_genomeMapped_transcriptome_Aligned.out.bam │ ├── endogenousAlignments_genomeMapped_transcriptome_Aligned.out.sorted.bam.coverage.txt │ ├── endogenousAlignments_genomeMapped_transcriptome_Log.final.out │ ├── endogenousAlignments_genomeMapped_transcriptome_Log.out.gz │ ├── endogenousAlignments_genomeMapped_transcriptome_Log.progress.out │ ├── endogenousAlignments_genomeMapped_transcriptome_SJ.out.tab │ ├── endogenousAlignments_genomeMapped_transcriptome_Unmapped.R1.fastq.gz │ ├── endogenousAlignments_genomeUnmapped_transcriptome_Aligned.out.bam │ ├── endogenousAlignments_genomeUnmapped_transcriptome_Log.final.out │ ├── endogenousAlignments_genomeUnmapped_transcriptome_Log.out.gz │ ├── endogenousAlignments_genomeUnmapped_transcriptome_Log.progress.out │ ├── endogenousAlignments_genomeUnmapped_transcriptome_Unmapped.R1.fastq.gz │ ├── endogenousAlignments_genome_Aligned.out.bam │ ├── endogenousAlignments_genome_Aligned.out.bam.CIGARstats.txt │ ├── endogenousAlignments_genome_Log.final.out │ ├── endogenousAlignments_genome_Log.out │ ├── endogenousAlignments_genome_Log.progress.out │ ├── filteringAlignments_UniVec_Aligned.out.bam │ ├── filteringAlignments_UniVec_Log.final.out │ ├── filteringAlignments_UniVec_Log.out │ ├── filteringAlignments_UniVec_Log.progress.out │ ├── filteringAlignments_UniVec_SJ.out.tab │ ├── filteringAlignments_rRNA_Aligned.out.sorted.bam │ ├── filteringAlignments_rRNA_Aligned.out.sorted.bam.bai │ ├── filteringAlignments_rRNA_Log.final.out │ ├── filteringAlignments_rRNA_Log.out │ ├── filteringAlignments_rRNA_Log.progress.out │ ├── filteringAlignments_rRNA_SJ.out.tab │ ├── readCounts_gencode_antisense.txt │ ├── readCounts_gencode_antisense_geneLevel.txt │ ├── readCounts_gencode_sense.txt │ ├── readCounts_gencode_sense_geneLevel.txt │ ├── readCounts_miRNAmature_sense.txt │ ├── readCounts_miRNAprecursor_sense.txt │ ├── readCounts_tRNA_sense.txt │ ├── testData_human.fastq.adapterSeq │ ├── testData_human.fastq.clipped.REMOVEDRepeatReads.fastq.gz │ ├── testData_human.fastq.clipped.fastq.gz │ ├── testData_human.fastq.clipped.trimmed.fastq.gz │ ├── testData_human.fastq.clipped.trimmed.filtered.fastq.gz │ ├── testData_human.fastq.clipped.trimmed.filtered.noRiboRNA.fastq.gz │ ├── testData_human.fastq.clipped.trimmed.filtered.noRiboRNA_fastqc.html │ ├── testData_human.fastq.clipped.trimmed.filtered.noRiboRNA_fastqc.zip │ ├── testData_human.fastq.clipped.trimmed.filtered.noUniVecContaminants.fastq.gz │ ├── testData_human.fastq.clipped.trimmed.filtered.rRNA.counts │ ├── testData_human.fastq.clipped.trimmed.filtered.rRNA.readCount │ ├── testData_human.fastq.clipped.trimmed.filtered.readLengths.txt │ ├── testData_human.fastq.clipped.trimmed.filtered.uniVecContaminants.counts │ ├── testData_human.fastq.clipped.trimmed.filtered.uniVecContaminants.readCount │ ├── testData_human.fastq.clipped.trimmed.filtered_fastqc.html │ ├── testData_human.fastq.clipped.trimmed.filtered_fastqc.zip │ ├── testData_human.fastq.knownAdapterSeq │ └── testData_human.fastq.qualityEncoding └── testData_human.fastq_CORE_RESULTS_v4.6.3.tgz ├── LICENSE ├── NCBI_Taxonomy.RData ├── README.md ├── _config.yml ├── exceRpt_Tools.jar ├── exceRpt_Tools ├── .gitignore ├── main │ ├── ExceRpt_Tools.java │ ├── ProcessEndogenousAlignments.java │ ├── ProcessExogenousAlignments.java │ └── QuantifyEndogenousAlignments.java └── src │ └── .DS_Store ├── exceRpt_coreDB ├── STAR_Parameters_Endogenous_smallRNA.in ├── STAR_Parameters_Exogenous.in ├── UniVec │ ├── STAR_INDEX_UniVec │ │ ├── Genome │ │ ├── SA │ │ ├── SAindex │ │ ├── chrLength.txt │ │ ├── chrName.txt │ │ ├── chrNameLength.txt │ │ ├── chrStart.txt │ │ └── genomeParameters.txt │ └── UniVec_Core.contaminants.fasta ├── adapters │ └── adapters.fa └── randomBits.dat ├── exceRpt_longRNA ├── exceRpt_smallRNA ├── mergePipelineRuns.R ├── mergePipelineRuns_functions.R ├── plotExogenous.R ├── plotExogenous_functions.R └── scriptsToMakeExogenousGenomes ├── combinePlants.sh ├── downloadFungi.sh ├── downloadPlants.sh ├── downloadProtists.sh ├── downloadVertebrates.sh ├── makeGenomes.txt ├── makeSTARIndex_Bacteria.sh ├── makeSTARIndex_FungiProtistVirus.sh ├── makeSTARIndex_Plants.sh ├── makeSTARIndex_Vertebrate.sh ├── source_step0 └── split_size.pl /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | .Rapp.history 3 | exceRpt_main 4 | -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- 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