Blat

From Augix' Wiki

BLAT Program Specifications

download blatSrc.zip unzip blatSrc.zip

echo $MACHTYPE
MACHTYPE=i386
export MACHTYPE
mkdir ~/bin/$MACHTYPE
make
cd ~/bin/i386/

faToTwoBit /mnt/biodata/mnt/expressions/augix/genomes/hg18/*.fa /mnt/biodata/mnt/expressions/augix/blat_database/twoBit/hg18.2bit

faToTwoBit /mnt/biodata/mnt/expressions/augix/genomes/panTro2/*.fa /mnt/biodata/mnt/expressions/augix/blat_database/twoBit/panTro2.2bit

gfServer start localhost 17779 /mnt/biodata/mnt/expressions/augix/blat_database/twoBit/hg18.2bit &
gfServer start localhost 17780 /mnt/biodata/mnt/expressions/augix/blat_database/twoBit/panTro2.2bit &

gfClient localhost 17779 \
 /mnt/biodata/mnt/expressions/augix/blat_database/twoBit/ \
 probe_fa/3040440.fa blat.3040440.hg.psl

more probe_fa/3040440.fa
 >3040440
 caagaggttgacagactcgatgacg

in R:

library(seqinr)
c2s(rev(comp(s2c("caagaggttgacagactcgatgacg"))))
[1] "cgtcatcgagtctgtcaacctcttg"

echo "16180964/50" | bc

cat /tmp/augix/hg18/chr19.fa | head -n 323623 | tail |\
 perl -pe "chomp;" | grep -i "cgtcatcgagtctgtcaacctcttg"