DGE¶
Quantification counting
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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 |
Expression Matrix expression_matrix
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input: | A list of count files (.txt) |
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output: | An expression matrix (.txt) |
script: | Reformats a list of count files into a genes x samples matrix |
Sample Renaming rename_samples
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input: | An expression matrix (.txt) |
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output: | An expression matrix (.txt) |
script: | Renames samples in expression matrix based on a user-supplied table |
Summary Report multiqc
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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 |