LRCAGE (long-read CAGE)

This repository contains scripts to call peaks, to retain a list of confident transcripts, and to build a proteome database for immunopeptidome analysis.

callpeak

a script to call peaks from LRCAGE, LRhex, and nanoCAGE data

usage: LRCAGE callpeak [-h] --inputlist INPUTLIST --peak PEAK
                       (--tpm TPM | --readcount READCOUNT) [--gcap GCAP]
                       [--gcap_mincount GCAP_MINCOUNT]
                       [--half_peak_width HALF_PEAK_WIDTH] [--thread THREAD]

optional arguments:
  -h, --help            show this help message and exit
  --inputlist INPUTLIST
                        list of input bam files
  --peak PEAK           output peak file name
  --tpm TPM             minimum TPM per peak
  --readcount READCOUNT
                        minimum read count per peak
  --gcap GCAP           minimum G-cap ratio
  --gcap_mincount GCAP_MINCOUNT
                        minimum number of soft-clipped G reads
  --half_peak_width HALF_PEAK_WIDTH
                        half peak size
  --thread THREAD       number of threads

filtertx

a script to retain a list of confident transcripts using transcripts identified from LRCAGE data and a list of peaks.

usage: LRCAGE filtertx [-h] --gtf GTF --talon TALON [--libinfo LIBINFO]
                       [--mincount MINCOUNT] [--peak PEAK]
                       [--peakratio PEAKRATIO] --oprefix OPREFIX

optional arguments:
  -h, --help            show this help message and exit
  --gtf GTF             input gtf file
  --talon TALON         input TALON.tsv file
  --libinfo LIBINFO     library size information
  --mincount MINCOUNT   minimum count to define confident transcripts
  --peak PEAK           peaks used to retain transcripts with complete 5' ends
  --peakratio PEAKRATIO
                        minimum fraction of reads for peak-transcript pair per
                        trancsript
  --oprefix OPREFIX     prefix for output files

buildprot

a script to create a proteome database using newly characterized transcripts as input.

usage: LRCAGE buildprot [-h] --gtf GTF --ref REF [--txinfo TXINFO]
                        [--thread THREAD] --oproteome OPROTEOME --refproteome
                        REFPROTEOME --refgtf REFGTF

optional arguments:
  -h, --help            show this help message and exit
  --gtf GTF             input gtf file
  --ref REF             reference genome fasta
  --txinfo TXINFO       transcript information
  --thread THREAD       number of threads
  --oproteome OPROTEOME
                        output proteome
  --refproteome REFPROTEOME
                        reference proteome
  --refgtf REFGTF       reference gtf

Run scripts using docker images

1. Download scripts from github

cd <your installation directory>
git clone https://github.com/juheon/LRCAGE.git

2. Download docker images from dockerhub

docker pull jhmaeng/lrcage
docker images ; See if you can find jhmaeng/lrcage

3. Modify and run “run_with_docker.sh” script in ”your installation directory”