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#Andy Rampersaud
#August 04, 2014
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#The following describes how to access the Waxman Lab VM (virtual machine) setup by CAS-IT (managed by: Sanborn, Jeffrey S <jsanborn@bu.edu>).
#The purpose of the VM is to store our UCSC Genome Browser data visualization files generated from High-throughput experiments.
#The VM provides a central location for data visualization file storage (BAM, bigWig, bigBed, etc...).
#Each lab member with a VM account is responsible for his/her own home directory.
#Data uploaded to the VM should be stored in your (/home/<your_username>/public_html) directory.
#See my example below for visualizing data on the UCSC Genome Browser from files stored on the VM.
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#VM Login Information
#Command line:
#The VM is setup so that users can use your BU login credentials
ssh <BU_Username>@waxmanlabvm.bu.edu
#OR
slogin <BU_Username>@waxmanlabvm.bu.edu
#My example:
#slogin aramp10@waxmanlabvm.bu.edu
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#After successful login, you will be in your respective home directory:
#My example:
#/home/aramp10
#I previously created some UCSC data files to visualize
#I put these file in my /public_html directory (/home/aramp10/public_html)
#Let's say I have the following file I want to visualize on the UCSC browser:
#G74C_M1_MACS2_peaks.narrowPeak.bb
#Step 1: Upload this file to the VM
#File location:
#/home/aramp10/public_html/G74C_G92_G99/G74C
#Step 2: Generate a track line
track type=bigBed name="G74C_M1_MACS2_narrowPeak_peaks" description="G74C_M1_MACS2_narrowPeak_peaks" visibility=squish color=0,0,0 bigDataUrl=http://waxmanlabvm.bu.edu/~aramp10/G74C_G92_G99/G74C/G74C_M1_MACS2_peaks.narrowPeak.bb
#Note with the above track line has the following http format:
#http://waxmanlabvm.bu.edu/~<your_username>/<file_location>
#Loading the above track line into the UCSC genome browser successfully visualizes the data
#Repeat the above process for however many data files that need to be visualized
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