Dear colleagues,
we now have the information of genomic features for many organisms, including the protein-coding genes, miRNAs, lncRNAs, et al, but new genes, especially the newly defined classes of genes, are identified continuously, for example, ascribed to the high tissue- and stage- specificity of lncRNAs, independent work would always identify hundreds or even thousands of new transcripts. Thus, we should resolve the problem, that when we annotated a large number of genes/transcripts ( include the annotated and unannotated genes/transcripts), how to merge these information with the exist annotation?
I have noticed the cuffmerge could do it in a way, but it would generate new transcripts when merging the GTFs, which is not expected sometimes.
Are there some other tools with a better performance? or any suggestion on parameter setting of cuffmerge?
Please clarify what you intend to do. Is the question about adding new transcripts to a file so that eventual redundancy is avoided and transcript names remain unique, keeping old transcript names; adding novel unique names only for new transcripts?
Or is the question rather about deposition of novel transcript variants in existing databases?
Or is it about creating an “updatable“ database that will ensure consistency with old annotation?
Katharina Hoff
mainly, the question is about how to add information of new isoforms to existed annotation, but 'add' is easy, my problem is about how to remove the redundant records with high accuracy and sensitivity.
The AUGUSTUS tool joingenes can do this (in principle; it’s a bit buggy). GeMoMa has the GAF module for similar purpose.
But it is quite easy to filter out redundancy using any scripting language. You simply build a string for each transcript that contains seq name, all exon coordinates and strand. Then use it as key in a hash/dict data structure for fast nonredundant storage. Print gtf file from hash or dict keys.
thank you Katharina Hoff. It is no doubt that your strategy is reasonable. We will try to figure it out if there is not any other available tool.
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