@@ -31,15 +31,15 @@ This SOP describes the analysis pipeline of downstream analysis of ChIP-seq sequ
## Design file
+ The Design file is a tab-delimited file with 4 columns for Single-End and 5 columns for Paired-End. Letter, numbers, and underlines can be used in the names. However, the names must begin with a letter. Columns must be as follows:
sample_id
1. sample_id
The id of the sample. This will be the header in output files, please make sure it is concise
experiment_id
2. experiment_id
Same name given for all replicates of treatment. Will be used for the consensus header.
replicate
3. replicate
Replicate number
fastq_read1
4. fastq_read1
Name of fastq file 1 for SE or PE data
fastq_read2
5. fastq_read2
Name of fastq file 2 for PE data
+ See [HERE](/docs/design_ENCSR451NAE_PE.txt) for an example design file, paired-end
