Update sample_data page.

website/docs/sample_data.md

@@ -2,19 +2,48 @@
 title: Sample Data
 ---
 
-A cohort containing `48` randomly selected experiments from ENCODE
-is available from the following page. 
+:::info
+The datasets used for testing and benchmarking MSPC, and 
+benchmarking results are available from _Open Science Framework (OSF)_
+at the following link.
+
+https://osf.io/jqrwu/
+:::
+
+We use data publicly available from ENCODE to test and benchmark 
+MSPC. This page outlines the specific experiments, our peak
+calling steps, and links to download the peaks we called and used
+for testing and benchmarking MSPC.
+
+### Dataset v2
+
+We benchmark MSPC v5 using a cohort containing `48` randomly selected 
+experiments from ENCODE. We call peaks on the samples in each 
+experiment using `MACS2` with a permissive threshold as the 
+following `--auto-bimodal -p 0.0001 -g hs`. This threshold 
+will result in a decreased number of false negatives, with the 
+penalty of an increased number of false positives. We will then 
+reduce the number of false positives while keeping 
+a low rate of false negatives, leveraging combined statistical 
+evidence from replicates (see the [methods page](method/about)).
+We use this cohort for testing MSPC v5.
+
+The peaks we called on this cohort are available from the 
+following page: 
 
 https://osf.io/jqrwu/
 
-[Download](http://www.bioinformatics.deib.polimi.it/genomic_computing/MSPC/packages/ENCODE_Samples.zip) 
-a dataset of test peaks (37 MB).
 
+### Dataset v1
 
-Peaks were called using [MACS2](http://liulab.dfci.harvard.edu/MACS/) with the arguments: `--auto-bimodal -p 0.0001 -g hs`.
+We benchmarked the [first version of MSPC](https://academic.oup.com/bioinformatics/article/31/17/2761/183989)
+using the dataset v1, which contains `7` experiments selected from ENCODE.
+We called peaks on this dataset using MACS2 with `--auto-bimodal -p 0.0001 -g hs`,
+and the called peaks are available from the following page: 
 
+https://osf.io/jqrwu/
 
-BAM files of the test samples were obtained from [ENCODE](https://www.encodeproject.org//):
+The following is the list of the BAM files of the samples in this dataset. 
 
 - [wgEncodeOpenChromChipK562CmycAlnRep1.bam](http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562CmycAlnRep1.bam) (412 MB);
 - [wgEncodeOpenChromChipK562CmycAlnRep2.bam](http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562CmycAlnRep2.bam) (286 MB);