# /data/images/bak/reczko/doc/fleming/panagiotou/marina/tg-dusp8.fa 
# has transgenic Dusp8 and WT Dusp8 (with introns+1kup+1kdown)

# all_dusp8.fa has format for IGV
cp /data/images/bak/reczko/doc/fleming/panagiotou/marina/all_dusp8.fa .
reczko@n2:/data/images/proton/GPlab/marina$ ln -s all_dusp8.fa tgDusp8.fa


# build bt2 index
/data/results/tools/align/bowtie2-2.2.3/bowtie2-build tgDusp8.fa tgDusp8

# align each sample
for i in *fq
do
echo $i
/data/results/tools/align/bowtie2-2.2.3/bowtie2 -a -p8 -x tgDusp8 $i  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - > $i.bam
done

samtools sort  GPR2-TgSal-786.fq.bam GPR2-TgSal-786.fq.sorted
samtools index  GPR2-TgSal-786.fq.sorted.bam 

samtools sort  GPR4-TgArs-787B.fq.bam GPR4-TgArs-787B.fq.sorted
samtools index GPR4-TgArs-787B.fq.sorted.bam