Manual Transcriptome Reconstruction Using Rna-Seq Reads (Hg19)

Question

[biorepine]

Dear Biostars,

I have been reconstructing novel coding or non-codng transcripts using either Cufflinks or Scripture from 2 years. They are very efficient tools to do de novo transcriptome reconstruction. However, sometimes both fail to do the job though there is more than enough RNA-Seq read coverage in an unannotated genomic region. I even noticed computationally predicted splice donor and acceptor sites overlapping these RNA-Seq reads. These features confirms that there is an expressed transcript but just missed by either cufflinks or scripture.

Now, is there anyway, I can manually design my transcript exons and introns using RNA-Seq mapped reads of a given genomic region ? I would really appreciate your suggestions on this.

Thanx in advance.

Answer 1

[Devon Ryan]

The regular annotation formats are text-based, so you can simply use a text editor to manually create them. It might be more interesting to find out why both cufflinks and scripture are missing these.