Proteotranscriptome pipeline

RNA-seq and proteomics integrated pipeline for identification of peptide evidence of Alu exon or Human specific exons
contact: ybwang@hust.edu.cn
Please leave message to me via email or report here https://github.com/Xinglab/proteoseq/issues if any questions
update: 2017-03-31

Requirements:

1. python 2.7.x or above, samtools
2. add samtools directory to the $PATH environment variable

Installation:

# download using the url: https://github.com/Xinglab/proteoseq/archive/master.zip 
unzip unzip proteoseq-master.zip
cd proteoseq-master
python install.py --homedir /u/home/y/ybwang --install directorToInstall

USAGE

Usage: ptp.py -b Aligned.out.sorted.bam -j SJ.tab.out -p proteomicsdir -e HSExonfile -o outdir
Parameter:
    -b bam file from STAR
    -j SJ.tab.out file from STAR
    -p proteomics dir
    -e exons file (bed format) or use 'None' to search all junctions peptide [default: None]
    -d database file to perform the MS comet search [default: data/Ensembl_Alu_25bp_0.5.unique.sorted.bed]
    -g genomic fasta directory [default: /u/home/f/frankwoe/nobackup/hg19/hg19_by_chrom/]
    -o output directory [default: outdir]
    --l Extend flanking junction ends by this number of bp
    --min-junc-reads Minimum number of reads required spanning the junction

Example

# search peptides from Alu exons
cd ~/scratch/ptptest
ln -s /u/home/f/frankwoe/nobackup/AST/Yoav_Gilad_YRI/RNA/star_output/GM18486.rna/ RNA
ln -s /u/home/y/ybwang/nobackup-yxing/data/Yoav_Gilad_proteom/GM18486/ PRO
python ptp.py -b RNA/Aligned.out.sorted.bam -j RNA/SJ.out.tab -p PRO/ -e data/Ensembl_Alu_25bp_0.5.unique.sorted.bed -d data/UP000005640_9606_additional_cdhit1.fasta -g /u/home/f/frankwoe/nobackup/hg19/hg19_by_chrom/

# or search for all junctions peptides:
python ptp.py -b RNA/Aligned.out.sorted.bam -j RNA/SJ.out.tab -p PRO/

# or submit the job using qsub
qsub -cwd -V -N PTP -l h_data=30G,h_rt=3:00:00 -M eplau -m bea ./example_submit.sh

Update (2017-03-31):

2017-03-31: update 'ptp.py' to support certain step start in pipeline
2017-03-30: modify important error in bin/percolator_triesearch_exon.py in 'def search()'
*. update ptp.py to support mzXML.gz, mzML.gz file input
*. modify 'percolator_test2parellel.py' to 'percolator_triesearch.py' to speed up the re-mapping step
*. output the result to file
*. modify the output on console