Reference-Guided Assembly of RNA-Seq Reads into Transcripts by Cufflinksa.

aCufflinks was employed to assemble reads into transcripts from each animal sample and Cuffcompare was used to obtain a union of transcripts from all 8 animals as summarized in this panel. ‘Total Transcripts Assembled’ was the sum of Complete, Partial and Novel transcripts. ‘Complete Match’ transcripts were identical to RefSeq transcripts (intron chain matches RefSeq gene); transcripts in the ‘Partially Match’ category include transcripts that overlap RefSeq transcripts but do not completely match (these could include potentially novel isoforms of an existing RefSeq transcript); and potentially ‘Novel’ transcripts are those that did not overlap with any RefSeq transcripts at all and may therefore involve intergenic transcripts.