1、软件安装
单独为leaf cutter创建一个环境 R版本为3.4.1(笔者操作系统为linux red hat,尝试了很多安装版本和方法，唯一可行的是：)
conda create -n r3.4.1 -y -c conda-forge r-base=3.4.1
conda activate r3.4.1
conda install -y -c conda-forge -c bioconda -c davidaknowles r-leafcutter
conda install bioconda::regtools
2、Differential Splicing
Step 0. Alignment
STAR --runThreadN 20 --genomeDir /index/mm10_GRCm38.101_index \
--readFilesIn $trim/${name}_clean_1P.fq $trim/${name}_clean_2P.fq \
--outFileNamePrefix $align/${name} --twopassMode Basic --outSAMstrandField intronMotif\
--outSAMtype BAM SortedByCoordinate --outBAMsortingThreadN 20 --quantMode TranscriptomeSAM GeneCounts
Step 1. Converting bams to juncs
##官方code
for bamfile in `ls run/geuvadis/*chr1.bam`; do
echo Converting $bamfile to $bamfile.junc
samtools index $bamfile
regtools junctions extract -a 8 -m 50 -M 500000 $bamfile -o $bamfile.junc
echo $bamfile.junc >> test_juncfiles.txt
done
