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#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