Further explanations in usage

Author: Kevin-Brockers

docs/usage.md

@@ -47,11 +47,13 @@ WT_INPUT,BLA203A30_S21_L002_R1_001.fastq.gz,,2,,,
 WT_INPUT,BLA203A31_S21_L003_R1_001.fastq.gz,,3,,,
 ```
 
-### Note on IP and control replicates
+### Note on IP and control replicates - Comparisons of one IP sample against multiple controls
 
 The pipeline is designed to handle one IP and matching control replicate, see section above. However there can be
 situations where one might want to make multiple comparisons of the IP sample against several different controls. In
-those cases it is advisable to encode these comparisons either in the sample column or as another replicate.
+those cases it is advisable to encode these comparisons either in the sample column or as another replicate. Since it is
+rather unusual in ChIP-Seq experiments, this feature is considered experimental. Please open a github issue in case you
+need further assistance.
 
 - Encoding in sample names:
 
@@ -119,15 +121,15 @@ NAIVE_INPUT,BLA203A48_S39_L001_R1_001.fastq.gz,,2,,,
 NAIVE_INPUT,BLA203A49_S1_L006_R1_001.fastq.gz,,3,,,
 ```
 
-| Column              | Description                                                                                                                                                                                                                                                                             |
-| ------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `sample`            | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). It should be unique and contain the antibody name. E.g: `{Treatment or cell type}_{antibody}_IP` |
-| `fastq_1`           | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                                                                                                                              |
-| `fastq_2`           | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                                                                                                                              |
-| `replicate`         | Integer representing replicate number. This will be identical for re-sequenced libraries. Must start from `1..<number of replicates>`.                                                                                                                                                  |
-| `antibody`          | Antibody name. This is required to segregate downstream analysis for different antibodies. Required when `control` is specified.                                                                                                                                                        |
-| `control`           | Sample name for control sample.                                                                                                                                                                                                                                                         |
-| `control_replicate` | Integer representing replicate number for control sample.                                                                                                                                                                                                                               |
+| Column              | Description                                                                                                                                                                                                                                                                                                                                                       |
+| ------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `sample`            | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). It should be unique per sample and contain sufficient informations, such as the antibody name. E.g: `{Treatment or cell type}_{antibody}_IP` -> `{WT/NAIVE}_{BCATENIN}_IP` |
+| `fastq_1`           | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                                                                                                                                                                                                        |
+| `fastq_2`           | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                                                                                                                                                                                                        |
+| `replicate`         | Integer representing replicate number. This will be identical for re-sequenced libraries. Must start from `1..<number of replicates>`.                                                                                                                                                                                                                            |
+| `antibody`          | Antibody name. This is required to segregate downstream analysis for different antibodies. Required when `control` is specified.                                                                                                                                                                                                                                  |
+| `control`           | Sample name for control sample.                                                                                                                                                                                                                                                                                                                                   |
+| `control_replicate` | Integer representing replicate number for control sample.                                                                                                                                                                                                                                                                                                         |
 
 Example design files have been provided with the pipeline for [paired-end](../assets/samplesheet_pe.csv) and [single-end](../assets/samplesheet_se.csv) data.