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STRTprep

STRTprep (https://github.com/shka/STRTprep) is an open-source software package for preprocess and analysis of STRT RNA-seq data. The first version was for the preprocessing and quality-check purposes, and the version 2 contains automated statistical tests of the differential expression. Furthermore, the version 3 will contain TFE-based quantification to analyze novel genes/start-sites including long-noncoding RNAs. This package can run on both Linux and OSX, and the typical protocol is as below.

git clone -b v3dev https://github.com/shka/STRTprep.git STRTprep3.test
cd STRTprep3.test
bin/install.sh
. bin/setup.sh
# pause; choose reference genome and transcriptome
bin/index_hg19_ercc92_ynbA_u13369.sh
bin/index_refGene.sh hg19 src/ebwt/hg19_ercc_ynbA_u13369/ref
# pause; edit conf.yaml and src/samples.csv
rake -m -j `gnproc` qc > qc.log 2>&1
# pause; check out/byGene/samples.xls
rake gene > gene.log 2>&1
# done! check out/byGene/diffexp.xls and do more further analysis!

The current version is 1; users can "try" the version 2 and 3.

Contents

1. Installation of STRTprep
2. Preprocessing and Analysis Protocol
3. Interpretation of the outputs