对298个lncRNAs进行miRNAs的预测

1.提取这298个lncRNAs的symbol

cat lncRNAs#部分lncRNAs
LINC02240
AC021723
AP003352
AC087393
AC006441
AC093503
AL121985
AC093484
AC145207
AC091180

2. 由starbase API数据库进行下载

time cat x1.csv |while read id;do echo $id;\
curl http://starbase.sysu.edu.cn/api/miRNATarget/?assembly=hg19\&geneType=lncRNA\&miRNA=all\&clipExpNum=0\&degraExpNum=0\&pancancerNum=0\&programNum=1\&program=PITA,RNA22\&target=${id}\&cellType=all > lncrna-mirna/$id.txt;
done

不到一分钟将全部lncRNA可能结合的miRNA下载到本地文件夹，文件大小为520B的都没有查询到可能结合的靶基因miRNA

ls -lh lncrna-mirna/
total 1.4M
-rw-rw-r-- 1 fqq1024 fqq1024  520 Aug 24 09:11 AC000120.txt
-rw-rw-r-- 1 fqq1024 fqq1024  520 Aug 24 09:11 AC002398.txt
-rw-rw-r-- 1 fqq1024 fqq1024  520 Aug 24 09:11 AC004543.txt
-rw-rw-r-- 1 fqq1024 fqq1024  520 Aug 24 09:11 AC004690.txt
-rw-rw-r-- 1 fqq1024 fqq1024  520 Aug 24 09:11 AC004784.txt

3.将所有的lncRNA靶基因进行合并整理

每个文件都有这么一个类似的表头

cat ZNF32-AS1.txt
#please cite:
#1.Zhou KR, Liu S, Cai L, Bin L, et al. ENCORI: The Encyclopedia of RNA Interactomes.
#2.Li JH, et al.starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data , Nucleic Acids Res. 2014 Jan;42:D92-7.
miRNAid miRNAname       geneID  geneName        geneType        chromosome      start   end     strand  clipExpNum      degraExpNum     RBP     merClass   miRseq  align   targetSeq       pancancerNum
The "target" parameter haven't been set correctly! Or the input of "target" parameter is not available!

合并所有的txt文件，并提取靶基因信息

cat *.txt > merge.txt
#删除注释行，删除行头，删除没有target的报错信息，
#最后获取第2例miRNA，第4例lncRNA
cat merge.txt |grep -v "#"|grep -v "chromosome"|grep -v "target"|cut -f2,4|less -SN
    1 hsa-miR-588     ACTA2-AS1
      2 hsa-miR-4701-5p ACTA2-AS1
      3 hsa-miR-378c    ACTA2-AS1
      4 hsa-miR-378a-3p ACTA2-AS1
      5 hsa-miR-422a    ACTA2-AS1
      6 hsa-miR-378h    ACTA2-AS1
      7 hsa-miR-378i    ACTA2-AS1
      8 hsa-miR-378d    ACTA2-AS1
      9 hsa-miR-378f    ACTA2-AS1
     10 hsa-miR-378b    ACTA2-AS1
     11 hsa-miR-378e    ACTA2-AS1
     12 hsa-miR-4428    ACTA2-AS1
     13 hsa-miR-3167    C21orf62-AS1
     14 hsa-miR-876-5p  C21orf62-AS1
     15 hsa-miR-627-5p  C21orf62-AS1