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LifeScope Genomic Analysis Solutions on Biowulf

LifeScope™ Genomic Analysis Software is a modular data analysis bioinformatics tool for performing off‐instrument secondary and tertiary analyses on sequence data generated by Life Technologies instruments. The resulting industry‐standard files from LifeScope™ Software can be used with third‐party visualization and analysis software tools.

LifeScope™ Software features:
• Seamless integration with the 5500 Series Genetic Analysis Systems
• Performance‐tuned algorithms for the 5500 Series and ECC module
• Optimized mapping and smaller file formats
• Annotated variant reports, numerous charts, and select visualization tools for simple data interpretation
• Ability to save and reuse workflows
• Ability to resume a workflow without repeating completed analyses
• Secure project‐based data management specific to your data analysis
• Projects can be stored and data reanalyzed

Data analyses Complementing LifeScope™ Software features are the following types of data analyses:
• Whole genome sequencing
• Targeted resequencing
• Low frequency variant
• Whole exome sequencing
• Whole transcriptome RNA sequencing
• Small RNA sequencing
• MethylMiner™ mapping
• CHiP‐Seq mapping
• Detection of wide range of genomic and RNA variation, including:
– SNP detection
– Large and small indel detection
– Copy number variation detection
– Inversion detection
– Fusion transcript detection
– Exon counting
– Splice finding

The current setting of lifescope on biowulf cluster is to run max of 3x 24gb nodes simultaneously.

How To Run

1. Contact staff@helix.nih.gov and ask for a lifescope account. Once the account is created, user can login to lifescope server and start submitting jobs to the cluster.

2. The following instructions are based on the example dataset. This dataset is available in /usr/local/lifescope/LSDF/testing. Copy the whole 'testing' directory into your own /data area.

$ mkdir /data/userID/lifescope $ cd /data/userID/lifescope $ cp -r /usr/local/lifescope/LSDF/testing .

3. login to the Biowulf head node.

YOUR PATH CAN NOT CONTAIN PATH TO BIOSCOPE!

For csh/tcsh users:

biowulf> set path=(/usr/local/lifescope/LSBF/lifescope/bin ${path})

For bash users:
biowulf> export PATH=/usr/local/lifescope/LSBF/lifescope/bin:$PATH

4. cd /data/userID/lifescope/testing/human_hg19, modify the 'global.ini' and 'readsets.rrs' files so that the path point to the right location in your /data/userID area.

5. While in /data/userID/lifescope/testing directory, with the $PATH variable set correctly as above, run this command from biowulf headnode. The script will automatically submit lifescope jobs to nodes for you.

$ lscope.sh run analysis.pln -u YourUserID -w lifescope

* 'run' tells lifescope server that you are in the 'run mode' of lifescope. There are several modes to run lifescope jobs. Biowulf only support 'run' mode.

* Your job will start a low memory process on biowulf headnode and several jobs will be submitted to the cluster for you.

* 'qstat -u YourUserID' & 'jobload -wc YourUserID' can be used to track your job progress.

 
Documentation

http://biowulf.nih.gov/apps/lifescope/LifeScope2_5_CmdLine4471875A.pdf

http://biowulf.nih.gov/apps/lifescope/4471877A_LifeScope_GUI_UG_2.5.pdf

http://biowulf.nih.gov/apps/lifescope/LifeScopeClusterQuickStart.pdf

http://biowulf.nih.gov/apps/lifescope/LifeScope_2.0_DataDrive_1.0_0624b.pdf

http://biowulf.nih.gov/apps/lifescope/LifeScopeWorkstationQuickStart-r5.pdf

http://biowulf.nih.gov/apps/lifescope/LifeScope_2.5_ReleaseNotes_1115a.pdf