Alternative tools for PacBio collapse_isoforms_by_sam.py

Question

[pengchy]

Dear all,

During the PacBio full length transcriptome data analysis process, one step is to collapse the sam files to get the unique isoform structure using collapse_isoforms_by_sam.py scripts. This script can be run from smrtlink package. However, the installation of smrtlink need root authority to designate a specific user ID for smrtlink package. So, I want to know whether it possible to run this script without installing smrtlink package, or there is an alternative standalone script to do the same work.

Best,

Answer 1

[pengchy]

This problem has been resolved by installation of: cDNA_Cupcake, which is easy to install and also contains collapse_isoforms_by_sam.py script