Scripture And Transcript Abundance

Question

[GPR]

Hello, Has anybody used Scripture to calculate transcript abundance? If so, how?

Answer 1

[dfernan]

Hi, Scripture is not recommended for transcript abundance, but rather transcriptome reconstruction.

A very good nature methods review, from Scripture's, and bowtie's main authors regarding different tools for transcript abundance is here: http://www.nature.com/nmeth/journal/v8/n6/abs/nmeth.1613.html.

Depending on what you are trying to do, for isoform abundance you could use (table 1 of the paper I recommended): Cufflinks, Miso or RSEM

Have a good day.

Answer 2

[GPR]

OK, thanks for your answer!