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zhangxudong 9c9ede5a62 修改参数顺序		2 ay önce
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README.md	20c01a01a2 add saf	8 ay önce
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run-featurecounts.R	9c9ede5a62 修改参数顺序	2 ay önce

一.安装

安装依赖R包 argparser, Rsubread, limma, edgeR
安装本软件

git clone http://git.genek.cn:3333/zhxd2/RunFeatureCounts.git

二.使用

对 GTF 中的 GENE 定量

Rscript RunFeatureCounts/run-featurecounts.R -b ../21.Mapping/BLO_S1_LD1.bam -g ../12.ref/genes.gtf -f exon -a gene_id -i FALSE -s 2 -o BLO_S1_LD1

对 GTF 中的 ISOFORM 定量

Rscript RunFeatureCounts/run-featurecounts.R -b ../21.Mapping/BLO_S1_LD1.bam -g ../12.ref/genes.gtf -f exon -a transcript_id -i FALSE -s 2 -o BLO_S1_LD1

对 SAF 定量

Rscript RunFeatureCounts/run-featurecounts.R -b aligned/FoxA1_E2_rep1_sorted_filtered.bam --saf merged_peaks.saf --isPairedEnd FALSE -o FoxA1_E2_rep1

README.md

一.安装

二.使用