Read counts were converted to FPKMs using total mapped reads for each dataset calculated by the SAMTools flagstat function and custom scripts. Transcripts not expressed at FPKM>1 in at least one dataset were removed. As a result of this FPKM>1 minimum filter, 99.975% of de novo assembled lincRNAs (pre-merging) have at least 5 reads supporting their expression in at least one of the combined datasets in Table S2, and >99.1% have at least 10 reads in one dataset. Transcripts were further categorized as FPKM>1, FPKM>10, and FPKM>30 in at least one dataset where each category is inclusive of all transcripts in higher categories.
