Rn5 Executing the Above Steps

Executing the Steps for new datasets for Rn5

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• Rat Star Consortium SNP Locations
  File generated by Steve Flink
  Located on Phenogen: /data/helicos/RatDNA/knownSnps/STAR_SNPs.uniqueMatch.bed

• Update Rat Exon SNP Masks

  • Download sequence information for the UCSC genome browser. It is easiest to download the files that are separated by chromosome
    Go to: [ftp://hgdownload.cse.ucsc.edu/goldenPath/rn5/bigZips/ rn5 download]
    Unfortunately there is no file that is separated by chromosome as of yet(if so, somebody point me in the right direction)
    Download file: rn5.2bit
    Saved file on Phenogen: /home/kiemele/HXB/UpdateRatGenome/rn5.2bit
  • Download probe sequence information from Affymetrix
    Go to: [http://www.affymetrix.com/estore/browse/products.jsp?productId=131489&categoryId=35748&productName=GeneChip-Rat-Exon-ST-Array#1_3 Affy Rat Exon1.0 ST Probe sequences]
    Download file: RaEx-1_0-st-v1.probe.fa.zip
    Saved file on Phenogen: /home/kiemele/HXB/UpdateRatGenome/RaEx1_0_st_v1.probe.fasta
  • Download and install BLAT
    Go to: [http://users.soe.ucsc.edu/~kent/src/ BLAT]
    Download: blatSrc35.zip (13 Aug 2012)
    Ended up having permission problems installing on server. Steve ended up giving me permission to use what he already installed.
  • Align probes to new genome
    General Code: blat database query output.psl
    On the Phenogen command line entered:
    Corrected:
    blat -stepSize=5 -minScore=20 -minIdentity=1 -repMatch=2253 /data/helicos/reference/rn5/noRandom/rn5_No_Random.fa RaEx1_0_st_v1.probe.fa output4.psl
    Previous Command Used:
    blat -stepSize=5 -minScore=20 -minIdentity=1 -repMatch=2253 RaEx1_0_st_v1.probe.fa /data/helicos/reference/rn5/noRandom/rn5_No_Random.fa output4.psl
    Note: lower minScore and minIdentity are required to get a higher number of perfect matches do not increase them assuming you are making filtering for perfect matches easier
    took about 5 hours to align
    Too big to load into R
    Can view on Phenogen server using some Basic Linux/Unix commands
  • Update masks
    Followed the outline above and updated code (saved on Lauren's desktop under: C:\Users\kiemelel\Documents\HXB\UpdateRatGenome\try20121012)

• Normalize Rat Exon Array Data Had problems accessing files under 2 different user names: see Basic Linux/Unix commands under Making Your Files Readable, Writable and Executable By Another User
  Got many errors:
  

  Ended up saving it to Tabastore file under Tabastore\Laura\BxH_HxB Rats\Exon Arrays\Brain\rn5\ Laura ran it under her user name on phenogen server with no problems

• Laura Saba beat me to calculating the heritability , eQTL with genome-wide and locus-specific pvalues and also generated LOD plots

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