Small RNA mapping

File name	Descrpition
snakemake/sequential_mapping.snakemake	Snakefile for sequential mapping. Required by snakemake/mapping_small.snakemake
${output_dir}/cutadapt/${sample_id}.fastq	Reads with adaptor trimmed
${output_dir}/tbam/${sample_id}/${rna_type}.bam	BAM files in transcript coordinates
${output_dir}/gbam/${sample_id}/${rna_type}.bam	BAM files in genome coordinates
${output_dir}/unmapped/${sample_id}/${rna_type}.fa.gz	Unmapped reads in each step
${output_dir}/fastqc/${sample_id}_fastqc.html	FastQC report file
${output_dir}/summary/fastqc.html	Summary report for FastQC (HTML)
${output_dir}/summary/fastqc.txt	Summary table for FastQC
${output_dir}/summary/fastqc.ipynb	Summary report for FastQC (Jupyter notebook)
${output_dir}/summary/read_counts.txt	Summary table for read counts
${output_dir}/stats/mapped_read_length_by_sample/${sample_id}	Length distribution of mapped reads

Long RNA mapping

File name	Descrpition
${output_dir}/cutadapt/${sample_id}.fastq	Reads with adaptor trimmed
${output_dir}/bam/${sample_id}/rRNA.bam	BAM files for reads mapped to rRNA
${output_dir}/bam/${sample_id}/genome.bam	BAM files for reads mapped to genome
${output_dir}/bam/${sample_id}/remove_duplicates.bam	BAM files for reads after removing duplicates
${output_dir}/bam/${sample_id}/circRNA.bam	BAM files for reads after removing duplicates
${output_dir}/unmapped/${sample_id}/${map_step}_1.fa.gz	Unmapped reads in each step
${output_dir}/fastqc/${sample_id}_fastqc.html	FastQC report file
${output_dir}/summary/read_counts.txt	Summary table for read counts
${output_dir}/stats/mapped_read_length_by_sample/${sample_id}	Length distribution of mapped reads
${output_dir}/stats/mapped_insert_size_by_sample/${sample_id}	Length distribution of mapped reads

Count matrix (small RNA-seq)

File name	Descrpition
${output_dir}/count_matrix/transcript.txt	Count matrix of transcripts
${output_dir}/count_matrix/htseq.txt	Count matrix of genes generated using HTSeq-count
${output_dir}/count_matrix/featurecounts.txt	Count matrix of genes generated using featureCounts
${output_dir}/counts_by_biotype/${count_method}/${sample_id}/${rna_type}	Gene/transcript counts generated using a feature counting tool

Long RNA domains

File name	Descrpition
${output_dir}/domain_counts/${bin_size}/${pvalue}/${sample_id}.bed	Read counts in long RNA domains (BED format with read counts in Column 5
${output_dir}/count_matrix/domain_${pvalue}.txt	Read count matrix of long RNA domains
${output_dir}/domains/${bin_size}/${pvalue}.bed	Long RNA domain locations
${output_dir}/domains_recurrence/${bin_size}/${pvalue}.bed	Recurrence of long RNA domains among samples (Column 5)

Matrix processing

File name	Description
${output_dir}/normalized_matrix/${normalization_method}.${imputation_method}.${batch_removal_method}.txt
${output_dir}/matrix_processing/normalization/${normalization_method}.txt
${output_dir}/matrix_processing/imputation/${normalization_method}.${imputation_method}.txt
${output_dir}/matrix_processing/batch_removal/${batch_removal_method}.${batch_index}.txt

Differential expression

File name	Description
${output_dir}/differential_expression/${count_method}/${compare_group}/${diffexp_method}.txt