Create new reference annotation merging different gtf files

[valeria11]

With Cuffcompare it is possible to determine a unique set of isoforms for each transcripts locus integrating different annotation resources. The problem is that Cuffcompare assigns new gene_id and transcripts_id for each transcript as "XLOC" and "TCONS". With the oId attribute in the new annotation it is possible to recover the gene_id and transcript_id code from the starting gtf file to have a complete new reference gtf file. In this new file each transcripts has all possible references to the relative annotation resource.

We have the same problem with Cuffmerge. With this tools the new detected isoforms are not changed in name but if the isoform name is "CUFF3.5" the relative gene_id name will be "CUFF3" and the transcripts_id "CUFF3.5".