Getting started

An example

The following is an example of using icSHAPE-pipe to calculate the activity score. The data and scripts are packaged in the .tar.gz file and click to download.

Example: human icSHAPE

Batch run

Users can run all commands directly with a written shell script at once.

• [icSHAPE-pipe]/bin/run-icpipe.sh: Run all commands in batches
• [icSHAPE-pipe]/bin/run-icpipe-lsf.sh: Run all commands in batches on the LSF cluster

run-icpipe.sh [-D D1.fastq,D2.fastq...] -N N1.fastq,N2.fastq... -f genome.fa -g genome.gtf -r rRNA.fa -a adaptor.fa -o outdir -p 20 -l 13 [-v]

run-icpipe-lsf.sh [-D D1.fastq,D2.fastq...] -N N1.fastq,N2.fastq... -f genome.fa -g genome.gtf -s ncbi/ensembl -r rRNA.fa -a adaptor.fa -o outdir -p 20 -l 13 -q [LSF-queue] [-v] [-c]

run-icpipe.sh and run-icpipe-lsf.sh run all steps of icSHAPE-pipe. You can ignore DMSO file (-D). Enter --help to see the detailed help information.