Detect differential transcripts between case and control from ONT data.
Step 0: set environment for LSF job on compute1 by adding the following to ~/.bashrc file:
export PATH=/storage1/fs1/songcao/Active/Software/anaconda3/bin:$PATH
export STORAGE2=/storage1/fs1/dinglab/Active export SCRATCH2=/storage1/fs1/dinglab/
export STORAGE1=/storage1/fs1/songcao/Active export SCRATCH1=/storage1/fs1/songcao/
export LSF_DOCKER_VOLUMES="$STORAGE1:$STORAGE1 $STORAGE2:$STORAGE2"
Step1: Enter the directory where you downloaded ONTsplice pipeline
Step2: Type the coommand line: perl ontsplice.ps.pl --rdir --ref --log --q --groupname --users --step
[0] pre-process bam
[1] Split bam
[2] Run espresso 1
[3] Run espresso 2
[4] Run espresso 3
[5] Merge espresso results from different chrs
[6] run sqanti
[7] re-run step espresso 3 by using new filtered gtf file from sqanti
[8] merge filtered espresso results
[9] run fsm
[10] re-run step espresso 3 based fsm results
[11] merge per chr results from 10 espresso results
[12] run rmats
[13] generate summary report
Example for running scripts:
perl ontsplice.ps.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/scor/analysis/run3 --log /storage1/fs1/dinglab/Active/Projects/scao/scor/analysis/run3.log -ref /storage1/fs1/songcao/Active/Database/hg38_database/sid.ont/all_sequences.fa --q general --users songcao --groupname SomaticWXS --step 1