ppbs

introduction

ppbs

ppbs is a toolkit for the rapid analysis and characterization of rna sequencing data. it utilizes a hybrid code based on gnu parallel, perl, bedtools, samtools, and tophat.

supports

read trimming ; genome mapping ; quantification (cds, intron, 3’utr, 5’utr), ; major annotation databases (refseq, ensembl, aceview) ; discovery of novel transcripts and transcriptionally active regions (tars) ; sequence variants (snps, indels) ; anti-sense transcription (directional rna-seq) ; quality metrics and summary data ; differential expression analysis ; publication-quality plots.