6.3 Transcriptome reconstruction and expression using cufflinks

There are a number of tools that perform reconstruction of the transcriptome and for this workshop you are going to use cufflinks, which can do transcriptome assembly with and without a reference annotation. It also quantifies the isoform expression in FPKMs. Let’s import the cufflinks module and check its (rather long) list of parameters:

$ module load cufflinks/2.1.1
$ cufflinks --help
 You are going to use cufflinks with the Ensembl annotation file for zebrafish limiting  the  transcriptome  reconstruction  strictly  to  the  available  annotations.  You  could  also   use the annotations as a guide but letting the algorithm look also for transcribed loci not  included in the annotations. In the first case cufflinks will only report isoforms that  are  included  in  the  annotation,  while  in  the  latter  case  it  will  report  novel  isoforms  as  well. First, copy the annotation file from Ensembl for chromosome 12 of Danio rerio: 

$ cp –r /pico/home/userexternal/fferre00/tutorial/annotations .  

Then let’s create a folder for the cufflinks output storage:

$ mkdir cuff_out