gsnap(genetech) install(설치)

1. 설치파일 다운로드

http://research-pub.gene.com/gmap/

2. root계정 활성화

su

3. 설치파일 압축풀기

tar xvzf gmap-gsnap-2017-01-14.tar.gz

4. configure 그리고 make 그리고 make install

cd gmap-gsnap-2017-01-14

./configure

make

make install

5. reference 파일 다운받기 및 reference build하기

wget ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz

gunzip -R Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz

gmap_build -d ens37.75_gsnap grch37.75_gsnap Homo_sapiens.GRCh37.75.dna.primary_assembly.fa

wget ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz

tar xvzf chromFa.tar.gz

gmap_build -d hg19_gsnap *.fa

# gmap 의 결과물은 다음의 장소에 생성됨 /usr/local/share/

6. splicing site다운받기 및 압축풀기

refgene

wget  ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz

gunzip -c refGene.txt.gz | psl_splicesites -s 1 > foo.splicesites

gunzip -c refGene.txt.gz | psl_introns -s 1 > foo.introns

gunzip -c refGene.txt.gz | psl_genes -s 1 > foo.genes

cat foo.splicesites | iit_store -o foo.splicesites_map

cat foo.introns | iit_store -o foo.introns_map

cat foo.genes | iit_store -o foo.genes_map

ensGene

wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ensGene.txt.gz

gunzip -c ensGene.txt.gz | psl_splicesites -s 1 > ensGene_splicesites

cat ensGene_splicesites | iit_store -o ensGene_spliceDB

gtf파일의 경우(ENSEMBL)

wget ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz

gunzip Homo_sapiens.GRCh37.75.gtf.gz

cat Homo_sapiens.GRCh37.75.gtf | gtf_splicesites > foo.splicesites

cat Homo_sapiens.GRCh37.75.gtf | gtf_introns > foo.introns

cat foo.splicesites | iit_store -o grch37.75_splicesites_map

cat foo.introns | iit_store -o grch37.75_introns_map

7. 돌리는 명령어

gsnap --db=grch37.75_gsnap --batch=5 --npath=1 -N 1 --nofails -Q -A sam --query-unk-mismatch=1 --use-splicing=/mnt/reference/gtf/grch37.75/foo.splicesites KN581_R_1.fq KN581_R_2.fq -o KNS81.sam

samtools -Sb KNS81.sam > KNS81.bam

samtools sort KNS81.bam KNS81.sorted.bam

--db : reference genome file

--use-splicing : splicing이 일어난다고 알려져 있는 거에 대한 table(refGene.txt)

끝

http://research-pub.gene.com/gmap/src/README