Rank Order

Giving an expression metrix, the rows are the genes and the columns are the strains.

1. calculate the means for each rows, save the result in an array, called means array
2. sort the means array by ascent
3. go back to the expression metrix, get every cell's rank by column
4. instead the cell expression value use the value of menas array that has the same rank with the cell

Annotation

1. the executable application is on Yan Cui's cluster, the folder is /home/rwilliams/blatSuite.
2. download the fa files from ucsc and unzip them in the folder
3. create the seqence file, see Illumina_Blat.fa
4. run blat, see t.sh

Liftover

1. create position file, each row should follow the format: chrX:Start-End. 'X' is chromosome, Start and End is basepair in integer format.
2. submit the position file to http://genome.ucsc.edu/cgi-bin/hgLiftOver
3. save 'View Conversions' as the new position, and 'Display failure file' as the failure positions

-- HongqiangLi - 05 Jan 2007