RSeQC鉴定文库是否为链特异性文库以及其他小功能

首先将基因组gtf文件转换为bed：

perl /media/shen/disk3/biosoft/gtf2bed/gtf2bed.pl gtf文件 > hg19.bed

脚本下载地址：https://github.com/ExpressionAnalysis/ea-utils/blob/master/clipper/gtf2bed

conda下载RSeQC：

source activate py2.7

conda install -c bioconda rseqc

infer_experiment.py -r hg19.bed -i align.bam

2. gene body coverage

geneBody_coverage.py -i 'Br_RNA1.bam' -r '/media/shen/disk1/jjc/reference/hg19/GRCh37-ERCC.bed' -o Br_RNA1_genebodycov