Alternative tools for PacBio collapse_isoforms_by_sam.py
1
0
Entering edit mode
3.3 years ago
pengchy ▴ 450

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,

PacBio sam collapse • 1.2k views
ADD COMMENT
0
Entering edit mode
3.3 years ago
pengchy ▴ 450

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

ADD COMMENT

Login before adding your answer.

Traffic: 3300 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6