Which One Is Better For Constructing Transcriptome For Noncoding Region, Scripture Or Cufflinks ?

Question

[camelbbs]

Hi all,

I want to ask does anyone have experience in constructing transcriptome for novel transcriptional regions, like lncRNA. I see both scripture and cufflinks can do that, but which one is better.

And if I find some novel transcriptional region, how to algin to lncRNA database to identify what they are, BLAST?

Thanks,

Che

Answer 1

[biorepine]

Both of them based on 2 different algorithms, scripture follows a segmentation approach and cufflinks a probabilistic approach. However, both Scripture and Cufflinks reconstruct the transcriptomes based on RNA-Seq reads that are aligned to the genome using a splicing read aligner (TopHat). The major difference is that, scripture is a very stringent method and doesn't report lowly expressed transcripts but cufflinks does. This is a key issue for lincRNAS because most of them are not higly expressed. For more information check this article. Regarding the second question, you need to download BLASTdb and have to compare your sequence with this database. A simple google search using "how to scan your sequence against a BLASTdb" will guide you. Hope that helps.

[camelbbs]

Thanks a lot! As that, cufflinks will find more lncRNA than scripture, right?

[biorepine]

it seems yes based on the above article.