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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. This package can run on both Linux and OSX.

... Edit two files to describe your experiment and study design, and run the pipeline as below, then you can finish from preprocessing until differential expression tests. Enjoy more further downstream analysis!

# STEP 1
## pause; decide name and the location of your project folder - now './STRTprep2.test'
git clone https://github.com/shka/STRTprep.git STRTprep2.test
cd STRTprep2.test
bin/install.sh
. bin/setup.sh
## pause; choose reference genome and transcriptome - now hg19 and RefSeq
bin/index_hg19_ercc92_ynbA_u13369.sh
bin/index_refGene.sh hg19 src/ebwt/hg19_ercc_ynbA_u13369/ref

# STEP 2
## pause; edit conf.yaml and src/samples.csv

# STEP 3
rake -m -j `gnproc` qc > qc.log 2>&1
## pause; check qc.log & out/byGene/samples.xls

# STEP 4
rake gene > gene.log 2>&1
## pause; check gene.log, out/byGene/diffexp.xls & out/byGene/plugins_*
##        go back to the step 2 when you would like to compare more

# DONE! Enjoy more further analysis!

The current version is 2, but version 3 beta (branch v3dev) is ongoing; the version 3 will provide TFE-based quantification to analyze novel genes/start-sites including long-noncoding RNAs.

Contents

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