expected_output.files

results/kallisto_indexes/homo_sapiens/kallisto.idx
results/salmon_indexes/homo_sapiens/31/salmon.idx/versionInfo.json
results/salmon_indexes/homo_sapiens/31/salmon.idx/duplicate_clusters.tsv
results/salmon_indexes/homo_sapiens/31/salmon.idx/info.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/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_adapters_mate1.fastq
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_polya_mate1.fastq
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_adapters_mate2.fastq
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_polya_mate2.fastq
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.SJ.out.tab
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/fastqc_data.txt
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/fastqc.fo
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/summary.txt
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/fastqc_data.txt
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/fastqc.fo
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/summary.txt
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/adapter_content.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/duplication_levels.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_base_n_content.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_base_quality.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_base_sequence_content.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_sequence_gc_content.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_sequence_quality.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_tile_quality.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/sequence_length_distribution.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/adapter_content.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/duplication_levels.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_base_n_content.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_base_quality.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_base_sequence_content.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_sequence_gc_content.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_sequence_quality.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_tile_quality.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/sequence_length_distribution.png
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/abundance.tsv
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/pseudoalignments.bam
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.kallisto.pseudo.sam
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/lib_format_counts.json
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/ambig_info.tsv
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/expected_bias
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/observed_bias
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/observed_bias_3p
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/unmapped_names.txt
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.remove_adapters_mate1.fastq
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.remove_polya_mate1.fastq
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.SJ.out.tab
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/fastqc_data.txt
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/fastqc.fo
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/summary.txt
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/adapter_content.png
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/duplication_levels.png
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/per_base_n_content.png
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/per_base_quality.png
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/per_base_sequence_content.png
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/per_sequence_gc_content.png
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/per_sequence_quality.png
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/per_tile_quality.png
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/sequence_length_distribution.png
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/abundance.tsv
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/pseudoalignments.bam
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.kallisto.pseudo.sam
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/lib_format_counts.json
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/ambig_info.tsv
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/expected_bias
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/observed_bias
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/observed_bias_3p
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/unmapped_names.txt
results/transcriptome/homo_sapiens/transcriptome.fa
results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMultiple.minus.bg
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMultiple.plus.bg
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.minus.bg
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.plus.bg
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMultiple.minus.bg
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMultiple.plus.bg
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.Unique.minus.bg
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.Unique.plus.bg
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMultiple_minus.bw
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMultiple_plus.bw
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Unique_minus.bw
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Unique_plus.bw
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMultiple_minus.bw
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMultiple_plus.bw
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_minus.bw
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_plus.bw
results/multiqc_summary/multiqc_data/multiqc_fastqc.txt
results/multiqc_summary/multiqc_data/multiqc_cutadapt.txt
results/multiqc_summary/multiqc_data/multiqc_cutadapt_1.txt
results/multiqc_summary/multiqc_data/multiqc_star.txt
results/multiqc_summary/multiqc_data/multiqc_kallisto.txt
results/multiqc_summary/multiqc_data/multiqc_general_stats.txt
results/summary_kallisto/tx2geneID.tsv
results/summary_kallisto/genes_counts.tsv
results/summary_kallisto/transcripts_counts.tsv
results/summary_kallisto/transcripts_tpm.tsv
results/summary_kallisto/genes_tpm.tsv