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TODO Jotting notes here

Samplemanifest

The following columns are required:

  • sample: sampleID; does not need to be a unique column
  • rep: replicateID of sampleID; does not need to be a unique column
  • fastq_1: absolute path to R1 of sampleID
  • fastq_2: absolute path to R1 of sampleID
  • antibody: -c sampleID for mac2; this must match a unique {sample}_{rep} format
  • control:

Example antibody / control format for a single-end project:

sample,rep,fastq_1,fastq_2,antibody,control
sample,1,/path/to/sample_1.R1.fastq.gz,,input_1,input_1
sample,2,/path/to/sample_2.R1.fastq.gz,,input_1,input_1
input,1,/path/to/sample1.R1.fastq.gz,,,
input,2,/path/to/sample1.R1.fastq.gz,,,

Example antibody / control format for a paired-end project:

sample,rep,fastq_1,fastq_2,antibody,control
sample,1,/path/to/sample_1.R1.fastq.gz,/path/to/sample_1.R2.fastq.gz,input_1,input_1
sample,2,/path/to/sample_2.R1.fastq.gz,/path/to/sample_1.R2.fastq.gz,input_1,input_1
input,1,/path/to/input_1.R1.fastq.gz,/path/to/input_1.R2.fastq.gz,,
input,2,/path/to/input_2.R1.fastq.gz,/path/to/input_2.R2.fastq.gz,,