Index of /examples/bioinformatics/cufflinks

Name	Last modified	Size

Parent Directory		-
accepted_hits.sam	2019-09-09 19:03	80K
cufflinks_job.qsub	2019-09-09 19:03	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/ Note: Research Computing Services (RCS) example programs are provided "as is" without any warranty of any kind. The user assumes the entire risk of quality, performance, and repair of any defects. You are encouraged to copy and modify any of the given examples for your own use.