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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. 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!

git clone https://github.com/shka/STRTprep.git STRTprep2.test
cd STRTprep2.test
bin/install.sh
. bin/setup.sh
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
rake gene > gene.log 2>&1

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.

• Documents for the version 2 - stable

• Documents for the version 3 - frequent updates; click "History" in the documents, then you can find difference between the previous updates.

• FAQ