scRNA-seq¶
Check Reads check_reads
¶
input: | List of read files (.fastq) |
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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) |
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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) |
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output: | Report files (.html) |
script: | Uses FastQC to check quality of read files |
Whitelist whitelist
¶
input: | List of read files (.fastq) |
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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) |
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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 |
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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) |
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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) |
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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) |
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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 |
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output: | A summary report (.html) |
script: | Uses MultiQC to generate a summary report |