Peaks2genes: modifications

topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.md

@@ -32,9 +32,9 @@ contributors:
 # Introduction
 {:.no_toc}
 
-We stumbled upon a paper [Li et al., Cell Stem Cell 2012](https://www.ncbi.nlm.nih.gov/pubmed/22862943) that contains the analysis of possible target genes of an interesting protein in mice. The targets were obtained by ChIP-seq and the raw data is available through [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37268).
-The list of genes however is neither in the supplement of the paper nor part of the GEO submission.
-The closest thing we could find is a list of the regions where the signal is significantly enriched (so called *peaks*):
+We stumbled upon a paper [Li et al., Cell Stem Cell 2012](https://www.ncbi.nlm.nih.gov/pubmed/22862943) called *"The histone acetyltransferase MOF is a key regulator of the embryonic stem cell core transcriptional network"*. The paper contains the analysis of possible target genes of an interesting protein called Mof. The targets were obtained by ChIP-seq in mice and the raw data is available through [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37268).
+However, the list of genes is neither in the supplement of the paper, nor part of the GEO submission.
+The closest thing we could find is a file in GEO containing a list of the regions where the signal is significantly enriched (so called *peaks*):
 
 1 | 3660676 | 3661050 | 375 | 210 | 62.0876250438913 | -2.00329386666667
 1 | 3661326 | 3661500 | 175 | 102 | 28.2950833625942 | -0.695557142857143
@@ -316,10 +316,12 @@ In order to convert the chromosome names we have therefore two things to do:
 
 ## Analysis
 
-Our goal is still to compare the 2 region files (the genes file and the peak file from the publication)
-to know which peaks are related to which genes. If you really only want to know which peaks are located **inside** genes you
-can skip the next step. Otherwise, it might be reasonable to include the promoter region into the comparison, e.g. because
-you want to include Transcriptions factors in ChIP-seq experiments.
+Our goal is to compare the 2 region files (the genes file and the peak file from the publication)
+to know which peaks are related to which genes. If you only want to know which peaks are located **inside** genes (within the gene body) you
+can skip the next step. Otherwise, it might be reasonable to include the **promoter** region of the genes into the comparison, e.g. because
+you want to include transcriptions factors in ChIP-seq experiments. There is no strict definition for promoter region but 2kb upstream of the TSS (start of region) is commonly used. We'll use the **Get Flanks** tool to get regions 2kb bases upstream of the start of the gene to 10kb bases downstream of the start (12kb in length). To do this we tell the Get Flanks tool we want regions upstream of the start, with an offset of 10kb, that are 12kb in length, as shown in the diagram below.
+
+![Get Flanks](../../images/intro_get_flanks.png)
 
 > ### {% icon hands_on %} Hands-on: Add promoter region to gene records
 >