Index of /examples/bioinformatics/cufflinks

Icon  Name                    Last modified      Size  Description
[DIR] Parent Directory - [   ] accepted_hits.sam 08-Mar-2015 19:49 80K [   ] cufflinks_job.qsub 08-Mar-2015 20:00 270

Cufflinks package example

To run Cufflinks at the command line:

scc4% module load cufflinks/2.2.1

scc4% cufflinks accepted_hits.sam
You are using Cufflinks v2.2.1, which is the most recent release.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File accepted_hits.sam doesn't appear to be a valid BAM file, trying SAM...
[19:50:03] Inspecting reads and determining fragment length distribution.
> Processed 1 loci. [*************************] 100%
> Map Properties:
> Normalized Map Mass: 90.00
> Raw Map Mass: 90.00
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[19:50:03] Assembling transcripts and estimating abundances.
> Processed 1 loci. [*************************] 100%


To submit a job, execute command:
scc4% qsub -P my_project cufflinks_job.qsub

Manual for Cufflinks:
http://cole-trapnell-lab.github.io/cufflinks/getting_started/