Method to identify novel transcript based on strand-specific RNAseq

Question

[biolab]

Dear all,

I have strand specific RNAseq data at hand, and aim to get novel transcripts being different from annotations. Apart from Cufflinks, is there any other tools to accomplish this job? Someone suggests me to use Trinity, but I think it's a de novo assembling tool. My data is based on a reference genome.

I appreciate any of your advice. THANKS.

Answer 1

[vivekbhr]

You can try Stringtie as a replacement for cufflinks.

[biolab]

Hi, Vivek, Thank you very much. I am going to take a try.