# Time-stamp: <2011-11-21 20:13:26 sunhf>

The files in this folder are for an RNA-Seq pipeline. 

1. Clone the pipeline from bitbucket:
$ hg clone https://bitbucket.org/hanfeisun/rna-seq-pipeline/

2. Make a copy of the origal rna.sample.conf as your own:
$ cp rna.sample.conf myRNA_pipeline.conf

3. Modify the 'ROOTDIR' key in 'Scrips' section to the download
folder. For example, you put the downloaded 'rna-seq-pipeline' folder
under '/scripts/pipeline' folder, then you should set the 'ROOTDIR' in
your conf file like this:


4. OK, that's all.

How to use
for test:

Just type in
$ python rnaseq_pipe.py rna.sample.conf

for your own use:

Create a config file follows the pattern in rna.sample.conf, and then
type in:
$ python rnaseq_pipe.py your_config.conf

Only want to have a look at the quality control
$ python rnaseq_pipe.py your_config.conf q

1. The pipeline can check whether you have made the right order of the
steps. For example, you should run Tophat before Cufflinks as
Cufflinks' input is Tophat's output. So if not sure about the order of
the steps in the pipeline, set the 'strict' key in 'strict' section to
True. The pipeline will stop immediately when it found something wrong
in the order.

rna-seq-pipeline 0.11		Nov 2011	Hanfei Sun