Differential RNA splicing analysis using leafcutter

Summary

Differential splicing analysis using leafcutter, one of the best tools.

Only works for hg19 or hg38.

Only works for paired-end RNA-seq data.

Input

Example data dir: Projects/Siqi_data/RNAseq_data/Differential_Exon_Analysis/test

1. fastq.tsv

3-col tsv, R1 R2 label.

Use run_lsf.py --guess_input to generate.

2. design.tsv

Two columns. First column should match to the labels in fastq.tsv. Second col is the group. Only pairwise. From leafcutter: Additional columns can be used to specify confounders, e.g. batch/sex/age. Numeric columns will be treated as continuous, so use e.g. batch1, batch2, batch3 rather than 1, 2, 3 if you a categorical variable.

2393110_Nontarget_Hudep2_2      WT
2393109_Nontarget_Hudep2_1      WT
2393111_Nontarget_Hudep2        WT
2393114_M1_Hudep2       sgRNA
2393113_M1_2_Hudep2_2   sgRNA
2393112_M1_2_Hudep2_1   sgRNA

Usage

    hpcf_interactive

module load python/2.7.13

run_lsf.py -f fastq.tsv -p leafcutter -g hg38 --design_matrix $PWD/design.tsv

Output

Results are stored in the $jid folder.

code @ github.