mir172 / mutationrater

Generate mutation rate according to alignments.

UCSC online database for genome https://genome.ucsc.edu/

Alignment File Format Described: (http://genome.ucsc.edu/goldenPath/help/chain.html)

Samples Download From FTP 1.hg38(human)-pantro4(chimp) alignement hg38.panTro4.all.chain.gz Format (http://genome.ucsc.edu/goldenPath/help/chain.html) 0 1 2 3 4 5 6 7 8 9 10 11 12 chain score tName tSize tStrand tStart tEnd qName qSize qStrand qStart qEnd id

2.Complete Genome Sequences By Chromosome hg38 -> chr1 http://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr1.fa.gz

UNCOMPRESS: gunzip .fa.gz

------sample get!!!

PyCuda module avail # view all module module load # load module

ssh cuda1, python is defautly loaded

module load cuda-5.5