An RPKM or TPM normalized matrix from LSTrAP can be directly used. Furthermore you should include sample
annotation.
Example for sample annotatation (note the header), two columns are required. The first is the sample ID,
as it occurs in the matrix (omit the suffix '.htseq'), the second column indicates the condition sampled.
SampleID ConditionDescription
SRR068956 Endosperm
SRR068957 Endosperm
SRR068958 Endosperm
SRR068959 Endosperm
SRR068971 Endosperm
SRR068975 Endosperm
SRR068976 Endosperm
SRR068977 Endosperm
SRR068987 Endosperm
...
Furthermore a file to color code tissues can be provided. Here for each condition a color (that will be
used in profile plots needs to be specified. Note that the order in this fill will be the order in
profile plots! Colors need to be in rgba(0-255,0-255,0-255,0-1) format.
Roots (apex), 7 DAG rgba(153, 51, 0, 0.5)
Roots (differentation zone), 4 DAP rgba(153, 51, 0, 0.5)
...