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 ...
...