results/kallisto_indexes/homo_sapiens/kallisto.idx
results/salmon_indexes/homo_sapiens/31/salmon.idx/duplicate_clusters.tsv
results/salmon_indexes/homo_sapiens/31/salmon.idx/hash.bin
results/salmon_indexes/homo_sapiens/31/salmon.idx/header.json
results/salmon_indexes/homo_sapiens/31/salmon.idx/refInfo.json
results/salmon_indexes/homo_sapiens/31/salmon.idx/rsd.bin
results/salmon_indexes/homo_sapiens/31/salmon.idx/sa.bin
results/salmon_indexes/homo_sapiens/31/salmon.idx/txpInfo.bin
results/salmon_indexes/homo_sapiens/31/salmon.idx/versionInfo.json
results/star_indexes/homo_sapiens/75/STAR_index/chrLength.txt
results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt
results/star_indexes/homo_sapiens/75/STAR_index/chrName.txt
results/star_indexes/homo_sapiens/75/STAR_index/chrStart.txt
results/star_indexes/homo_sapiens/75/STAR_index/exonGeTrInfo.tab
results/star_indexes/homo_sapiens/75/STAR_index/exonInfo.tab
results/star_indexes/homo_sapiens/75/STAR_index/geneInfo.tab
results/star_indexes/homo_sapiens/75/STAR_index/Genome
results/star_indexes/homo_sapiens/75/STAR_index/SA
results/star_indexes/homo_sapiens/75/STAR_index/SAindex
results/star_indexes/homo_sapiens/75/STAR_index/sjdbInfo.txt
results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.fromGTF.out.tab
results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.out.tab
results/star_indexes/homo_sapiens/75/STAR_index/transcriptInfo.tab
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_adapters_mate1.fastq
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_adapters_mate2.fastq
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_polya_mate1.fastq
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_polya_mate2.fastq
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_SJ.out.tab
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/fastqc_data.txt
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/fastqc.fo
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/summary.txt
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/adapter_content.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/duplication_levels.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_n_content.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_quality.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_sequence_content.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_sequence_gc_content.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_sequence_quality.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_tile_quality.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/sequence_length_distribution.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/fastqc_data.txt
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/fastqc.fo
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/summary.txt
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/adapter_content.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/duplication_levels.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_base_n_content.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_base_quality.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_base_sequence_content.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_sequence_gc_content.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_sequence_quality.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_tile_quality.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/sequence_length_distribution.png
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/abundance.tsv
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/pseudoalignments.bam
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/synthetic_10_reads_paired_synthetic_10_reads_paired.kallisto.pseudo.sam
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/lib_format_counts.json
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/aux_info/ambig_info.tsv
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/aux_info/expected_bias
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/aux_info/observed_bias
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/aux_info/observed_bias_3p
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/aux_info/unmapped_names.txt
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.remove_adapters_mate1.fastq
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.remove_polya_mate1.fastq
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_SJ.out.tab
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/fastqc_data.txt
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/fastqc.fo
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/summary.txt
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/adapter_content.png
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/duplication_levels.png
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_n_content.png
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_quality.png
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_sequence_content.png
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_sequence_gc_content.png
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_sequence_quality.png
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_tile_quality.png
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/sequence_length_distribution.png
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/abundance.tsv
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/pseudoalignments.bam
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.kallisto.pseudo.sam
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/lib_format_counts.json
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/quant.genes.sf
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/quant.sf
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/ambig_info.tsv
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/expected_bias
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/observed_bias
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/observed_bias_3p
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/unmapped_names.txt