scRNA-seq

Check Reads check_reads

input:List of read files (.fastq) output:None script:Ensures correct format of sequencing read files

Genome Indexing hisat_indexing/star_indexing

input:Genome reference file (.fa) | Genome annotation file (.gtf) output:Directory containing indexed genome files script:Uses either STAR or HISAT2 to build an indexed genome

Quality Check fastqc

input:List of read files (.fastq) output:Report files (.html) script:Uses FastQC to check quality of read files

Whitelist whitelist

input:List of read files (.fastq) output:A table of white listed barcodes (.txt) script:Uses UMI-tools to extract and identify true cell barcodes

Extract extract

input:List of read files (.fastq) | A table of white listed barcodes (.txt) output:Extracted read files (.fastq) script:Uses UMI-tools to extract barcode from reads and append to read name

Read Mapping hisat_mapping/star_mapping

input:List of read files (.fastq) | Genome annotation file (.gtf) | Directory containing indexed reference genome files output:A list of alignment files (.bam) | Log files (.log) script:Uses either STAR or HISAT2 to align reads to a reference genome

Reformat Reference gtftobed

input:Genome annotation file (.gtf) output:Genome annotation file (.bed) script:Converts genome annotation file from GTF to BED format

Mapping Quality rseqc

input:A list of alignment files (.bam) output:Report files (.txt) script:Uses RSeQC to check quality of alignment files

Quantification counting

input:A list of alignment files (.bam) | Genome annotation file (.gtf) output:Read counts (.txt) | Log files (.txt) script:Uses featureCounts to quantify reads

Summary Report multiqc

input:Log files and summary reports from all processes output:A summary report (.html) script:Uses MultiQC to generate a summary report