Merging the transcript annotations of the sexes yields a total of 16,261 predicted transcripts from 11,356 genes.
First cufflinks was used to assemble transcripts for each sample using the fr-firststrand option, followed by Cuffmerge to merge the assembled transcripts from all samples with the reference transcripts.
Cuffmerge was used to merge the assembled transcripts from the two biologically independent samples.
Cuffmerge was used to merge the assembled transcripts into a consensus gene track from the all of the mapped samples.
Yet in part also due to the strong focus to merge the layers in transcripts, which prompted the identification of ways of representing and communicating talk, environment and emic perspectives that added to and deepened the previous layers.
Cuffmerge and Cuffdiff [ 49, 50] were then used for prediction of genes by merging the predicted transcripts in the four tissues, allowing for comparison of FPKM values in the four transcriptomes at each predicted gene locus.
"Blocks" located within an annotated gene not separated by introns are merged reducing the transcript "fragmentation".
These annotations were merged at the transcript cluster level (see 'Microarray and Gene Expression Analysis'), which means that GO-terms associated with isoforms were propagated onto the canonical transcript.
Annotated and novel lncRNAs were present in similar proportions in these sets, supporting the validity of our strategy of merging the two types of transcripts from the beginning.
We merged the CDS predicted from transcripts of genome-guided and genome-independent assemblies to obtain a single comprehensive reference combining advantages from both assembly methods.
