Documentation test data updated

test/README.md

@@ -1,17 +1,49 @@
 # Data for running Nucleosome Dynamics
 
-Nucleosome dynamics can be tested with the sample input data you find at `test/data`. It includes:
+We describe here the files required to run Nucleosome Dynamics and provide sample input data that can be used to test the code. The directory `test/data` includes:
 
-1. MNase-seq reads
+1. Sample MNase-seq reads
 2. Reference genome associated data
 
 #### 1. MNase-seq reads
 
-`test/data/cellcycle*` files are sample MNase-seq reads aligned BAM files. 
-TDB
+`test/data/cellcycle*` BAM files contain mapped reads to R64-1-1 genome assembly, from an MNaseSeq experiment published in Deniz et al. (2016) for S. cerevisiae chrII in G2 and M cell cycle phases. 
+
+YBD
+BAM files should be indexed to be read with nucleR function readBAM function?
 RData and BAI files are needed?
 Do we want to include output sample data?
 
 #### 2. Reference genome associated data
 
-TDB
+Two files are requiered for the corresponding genome assembly:
+
+* Chromosome sizes: two-column tab-separated text file containing assembly sequence names and sizes. It can be downloaded from [UCSC](http://hgdownload.soe.ucsc.edu/downloads.html)
+* Gene TSS and TTS coordinates: GFF3 file containing information for every gene. For a full description of the fields in GFF3 files see [ensemle](https://www.ensembl.org/info/website/upload/gff3.html) website. The following columns are required:
+  * seqid: name of the chromosome in the corresponding genome assembly
+  * source: name of the program that generated this feature, or the data source. If not provided, it should be denoted with '.'
+  * type: type of feature. If not provided, it should be denoted with '.'
+  * start: start point of the feature. Should correspond with TSS for genes in the + strand, TTS for the genes in the + strand
+  * end: end point of the feature. Should correspond with TTS for genes in the + strand, TSS for the genes in the + strand
+  * score: not required (it should be denoted with '.')
+  * strand: defined as + (forward) or - (reverse)
+  * phase: not required (it should be denoted with '.')
+  * attributes: a semicolon-separated list of tag-value pairs, providing additional information about each feature. At least three values are required: 
+    * name: gene identifier
+    * tss: TSS of the gene
+    * tts: TTS of the gene
+
+We provide the files for S. cerevisiae genome assembly R64-1-1 in `test/data/refGenomes/R64-1-1`. Chromosome sizes were downloaded from [SGD](http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-1-1_20110203.tgz) and gene TSS and TTS were compiled from Pelechano et al. (2013), Miura et al. (2006), Yassour et al. (2009), Nagalakshmi et al. (2008).
+
+
+# References 
+Deniz, O., Flores, O., Aldea, M., Soler-López, M., and Orozco, M. (2016). Nucleosome architecture throughout the cell cycle. Scientific Reports 6, 19729.
+
+Pelechano, V., Wei, W., Steinmetz, L.M. (2013). "Extensive transcriptional heterogeneity revealed by isoform profiling." Nature, 497, pp. 127–131. doi: 10.1038/nature12121
+
+Miura, F., Kawaguchi, N., Sese, J., Toyoda, A., Hattori, M., Morishita, S., Ito, T. (2006). "A large-scale full-length cDNA analysis to explore the budding yeast transcriptome." Proc. Natl. Acad. Sci. U.S.A., 103, pp. 17846–17851. doi: 10.1073/pnas.0605645103
+
+Yassour, M., Kaplan, T., Fraser, H.B., Levin, J.Z., Pfiffner, J., Adiconis, X., Schroth, G., Luo, S., Khrebtukova, I., Gnirke, A., Nusbaum, C., Thompson, D.-A., Friedman, N., Regev, A. (2009). "Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing." Proceedings of the National Academy of Sciences, 106, pp. 3264–3269. doi: 10.1073/pnas.0812841106
+
+Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., Snyder, M. (2008). "The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing." Science, 320, pp. 1344–1349. doi: 10.1126/science.1158441
+