Question: Manual Transcriptome Reconstruction Using Rna-Seq Reads (Hg19)
gravatar for biorepine
7.1 years ago by
biorepine1.5k wrote:

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.

cufflinks rna-seq • 2.4k views
ADD COMMENTlink modified 7.1 years ago by Devon Ryan96k • written 7.1 years ago by biorepine1.5k
gravatar for Devon Ryan
7.1 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

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.

ADD COMMENTlink written 7.1 years ago by Devon Ryan96k
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