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@@ -24,6 +24,8 @@ b) Reference preparation: |
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`$ lib/bismark_v0.12.3/bismark_genome_preparation sequences/hg19`
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-2) Running a sample:
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+2) Run pipeline on a sample directory (containing paired-end files of the form: `<SAMPLE>_L001_R1_001.fastq.gz`, `<SAMPLE>_L001_R2_001.fastq.gz`):
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`$ src/bis_seq/run_sample.sh hg19 /path/to/sample/`
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+
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+ - Expects files within the directory of the form:
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