11/11/2014

the following bugs have been fixed:

• unnecessary step for non-stranded data removed
• runall_normalization.pl modified
• samtools location needs to be specified in the config file
• fixed get_percent_numchr.pl to work with all chr names
• unique merge sam for gene norm fixed

v0.6-beta - 11/5/2014

• New config file.
• Exon-Intron-Junction Normalization outputs normalized exonmappers, intronmappers, and intergenicmappers separately (instead of outputting one final normalized sam/bam file for each sample).
• PORT now supports stranded data. Sense and antisense spreadsheets and sam/bam files will be provided at the end of the pipeline.
• Highly expressed introns added to the list of normalization factors.

v0.5-beta - 9/28/14

• Gene Normalization/Quantification and Exon-Intron-Junction Normalization/Quantification done separately.
• Normalization factors stats file combines all normalization factor statistics into one file.
• Filter high expressors removes reads that map to the high expressors.
• Config file updated.

v0.4-beta - 8/26/14

• resume and -resume_at option added
• label novel exons in exon counts spreadsheet
• gene coordinates added to gene counts spreadsheet

v0.3-beta - 8/11/2014

• Gene-level quantification step added (this will output FINAL_master_list_of_genes_counts_MIN and MAX)

v0.2-beta - 8/6/2014

• Organized/rearranged the pipeline into PART1 and PART2
• Read number prediction more accurate (unique reads), happens later in the pipeline
• Users have option to check the read numbers/high expressors before running steps in PART2
• Added strand-specific coverage option (can be set in the config file)
• Fixed bugs (compress step and runall_shuf.pl script)