Transcriptome Reannotation Pipeline based on RNA-Seq..

[mhadidi2002]

Hello All,

I would like to share my ideas with you, and ask for you suggestions..

Thanks to Transcriptome reconstruction programs like Cufflinks and Scripture, and provided that we have RNA Seq reads, we can reconstruct the whole transcriptome and/or genome without a need to sequence the whole genome.

The main problem is that after using cufflinks for example, it produce GTF files with annotations for genes positions and isoforms. the problem is that some times when comparing the already published annotations with the annotations we have from cufflinks, they may be different. here we have to decide which is right and which is wrong in order to do reannotations for transcriptome/genome (in case the organism is poorly annotated)

Does any one know a method that we can use to decide which annotations are true? How can we judge which annotations is better?

I would like to hear your opinions regarding this issue..

[arvid]

I would align read data from several different tissues, experimental conditions, labs and sequencing technologies to see which annotation has the best support. Then choose a number of loci on random and check them by PCR in the lab...