gtf等文件下载

1. 下载gtf文件
   另外可根据如下网址，直接下载，以小鼠为例，可以一步步向上文件夹打开

https://ftp.ensembl.org/pub/release-109/gtf/mus_musculus/Mus_musculus.GRCm39.109.gtf.gz

2. 下载tss.bed文件

hg38
#下载地址，下载refFlat.txt.gz
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refFlat.txt.gz
#转为bed文件
zcat refFlat.txt.gz | awk '{print $3"\t"$5"\t"$6"\t"$1"\t"$4}' > hg38.tss.bed
# 只保留确定位置的片段
awk '/chr[0-9XY]{1,2}\t/' /Users/guoyin/hg38.tss.bed > /Users/guoyin/hg38_filter.tss.bed

hg19
#下载地址，下载refFlat.txt.gz
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz
#转为bed文件
zcat refFlat.txt.gz | awk '{print $3"\t"$5"\t"$6"\t"$1"\t"$4}' > hg19.tss.bed
awk '/chr[0-9XY]{1,2}\t/' /Users/guoyin/hg19.tss.bed > /Users/guoyin/hg19_filter.tss.bed

3. hg38 坐标转换到 hg19 坐标
   下载网址：https://hgdownload.soe.ucsc.edu/downloads.html#human
   Other downloads----Utilities

cd atac_fragments.tsv.gz
gzcat atac_fragments.tsv.gz | head -1000 > atac_hg38.bed
cat atac_hg38.bed | head -10
wget hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz
gzcat hg38ToHg19.over.chain.gz | less
# wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver
# wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/liftOver
chmod +x liftOver
./liftOver atac_hg38.bed hg38ToHg19.over.chain.gz atac_hg19_translated.bed atac_hg19_lost.bed

4. 给fragments.tsv.gz创建fragments.tsv.gz.tbi

# gzip -d atac_hg19_translated.bed.gz 
sort -k1,1 -k2,2n -k3,3n atac_hg19_translated.bed > atac_hg19_translated.sorted.bed
bgzip atac_hg19_translated.sorted.bed
tabix -p bed atac_hg19_translated.sorted.bed.gz