#pyrnatools

Installation

Clone this repository and then:

$ cd pyrnatools/
$ python setup.py install --user

This will install the scripts in the pyrnatools/scripts directory. For more information on the individual scripts, use the --help command after each script.

##Core Pipeline

• pyrna_align.py -> Wrapper for FASTQC, cutadapt and tophat2 sequence aligner
• pyrna_count.py -> Wrapper for Htseq-count and gfold-count
• pyrna_diff.py -> Wrapper for deseq2/gfold differential expression analysis
• pyrna_ucsc.py -> Converts bam file to UCSC formatted bigWig

##Additional Tools

• pyrna_pair_tools.py -> Infers sample orientation and calculates insert size for paired end RNA-seq data
• pyrna_denovo.py -> Cufflinks wrapper for denovo assembly
• pyrna_download.py -> Tool for downloading samples from GEO