updated docs

README.md

@@ -10,8 +10,8 @@ LSTrAP wraps multiple existing tools into a single workflow. To use LSTrAP the f
 
 ![LSTrAP Workflow](docs/images/LSTrAP_workflow.png "Steps automated by LSTrAP")
 
-Steps in bold are submitted to a cluster. Optional steps can be enabled by adding the flag *--enable-interpro* and/or 
-*--enable-orthology*.
+Steps in bold are submitted to a cluster. Optional steps can be enabled by adding the flag *‑‑enable‑interpro* and/or 
+*‑‑enable‑orthology*.
 
 ## Preparation
 
@@ -70,6 +70,13 @@ steps prior to building the network.
 
 More information on how the quality of samples is determined can be found [here](docs/quality.md).
 
+## Output
+
+Apart from the output all tools included generate, LSTrAP will generate raw and normalized expression matrices, a 
+co‑expression network and co‑expression clusters.
+
+A detailed overview of files produces, including examples, can be found [here](docs/example_output.md).
+
 ## Helper Scripts
 
 LSTrAP comes with a few additional scripts to assist users to download and process data from the [Sequence Read Archive](http://www.ncbi.nlm.nih.gov/sra),

docs/example_output.md

@@ -0,0 +1,55 @@
+# Example output
+
+Upon completion, LSTrAP will have run Trimmomatic, Bowtie 2, TopHat2 and HTSeq-Count. Unless specified otherwise, the 
+raw output from those tools will be stored. Furthermore, LSTrAP further processes the output of these tools to construct
+expression matrices, co-expression networks and clusters. A description of the LSTrAP specific output can be found 
+below.
+
+## Expression profiles/matrix
+
+LSTrAP will write the raw expression matrix as well as an RPKM and TPM normalized version upon completion. This is a 
+large matrix where columns (separated by tabs) are samples and rows are transcripts. In each cell the raw or normalized expression value 
+is included. Mock example is included below.
+
+A single row, along with the header, can be used to draw an expression profile (cfr. in Excel, R, ...)
+
+    gene    Sample1 Sample2 Sample3 ... Sample10
+    Gene1   2       1       3       ... 0
+    Gene2   0       0.5     0       ... 0
+    Gene3   2       0.22    0.11    ... 0.5
+    ...     ...     ...     ...     ... ...
+    Gene10  1       3       0       ... 0.7            
+
+## Co-expression network
+
+Pearson's Correlation Coefficients (PCC) are calculated based on the TPM normalized expression matrix. A file is written
+where for each transcript (ID before the colon) the top 1000 co-expressed genes (ID after colon, tab separated) are shown with the PCC value 
+(number between round brackets).
+
+    AT1G05660.1: AT1G06120.1(0.975109345421)        AT4G01630.1(0.971643917372)     AT3G59130.1(0.967450941397)     AT2G39040.1(0.961912892051)     AT2G43880.1(0.958996761442) ...
+    AT5G09780.1: AT3G17010.1(0.949034133987)        AT5G57720.1(0.870169887662)     AT2G16210.1(0.8604233184)       AT5G47600.1(0.818799585331)     AT5G37860.1(0.801435539475) ...
+    AT2G19740.1: AT3G02560.1(0.842648087998)        AT5G28060.1(0.837579535602)     AT5G56710.1(0.835775366218)     AT2G44860.1(0.828341737973)     AT2G39460.1(0.828069004117) ...
+    ...
+
+Furthermore, the co-expression network is prepared for MCL clustering. Here only co-expressed pairs with PCC 
+values > 0.7 are considered. The score stored in this file is PCC - 0.7 as MCL requires the minimal value to be zero.
+On each line you have two co-expressed genes and the correlation transformed for use with mcl. This file can be imported
+into Cytoscape desktop or Gephi for visualization/further analysis. 
+
+    AT1G67450.1     AT4G23110.1     0.0496500079172
+    AT1G67450.1     AT4G05630.1     0.0490984038043
+    AT1G67450.1     AT5G40430.1     0.0479090219126
+    ...
+
+# Co-expression clusters
+
+Co-expression clusters, detected using MCL, are stored as a text file where each line represents a co-expression 
+cluster. IDs for transcripts belonging to that cluster are separated by tabs. 
+
+    AT2G19740.1     AT3G02560.1     AT5G28060.1     AT5G56710.1     AT2G44860.1     AT2G39460.1     AT1G34030.1     AT1G26880.1     AT3G28900.1     AT3G04920.1 ...
+    AT1G69250.1     AT1G52640.1     AT5G15820.1     AT1G17130.1     AT3G24210.1     AT5G27330.1     AT4G21140.1     AT4G12610.1     AT5G49000.1     AT4G25340.1 ...
+    AT1G27500.1     AT1G04700.1     AT3G24715.1     AT3G57140.1     AT4G07960.1     AT2G30505.1     AT1G79860.1     AT1G44120.1     AT1G05820.1     AT1G52240.1 ...
+    AT2G40030.1     AT3G51290.1     AT4G39600.1     AT2G02790.1     AT3G07200.1     AT2G27040.1     AT5G14610.1     AT3G17840.1     AT2G39620.1     AT2G40720.1 ...
+    AT5G05657.1     AT2G16881.1     AT3G23650.1     AT4G23103.1     AT4G08370.1     AT3G24216.1     AT2G02280.1     AT3G31068.1     AT2G01780.1     AT2G03932.1 ...
+    AT1G32520.1     AT4G09350.1     AT1G62250.1     AT3G47430.1     AT2G37240.1     AT2G04039.1     AT2G35660.1     AT5G09660.1     AT2G39730.1     AT4G26860.1 ...
+    ...