PORT v0.8.5e-beta 03/24/2021

[config file]

• No change since previous version

[bug fixes]

• Fix precedence issue warnings generated by some versions of Perl. These caused PORT to stall.

PORT v0.8.5d-beta 10/25/2018

• PORT is now under GNU GPL v3.0

PORT v0.8.5c-beta 05/11/2018

[config file]

• same as v0.8.5b-beta

[bug fixes]

• Minor fixes for log file and stat file generation.

PORT v0.8.5b-beta 04/11/2018

[config file]

• Added info about config requirements for re-running part II of PORT.
• Compatible with config files from v0.8.3-beta, or greater.

[bug fixes]

• Minor correction to genepercents calculation for single-end data.
• Assorted errors stemming from use of mkdir and echo commands that cause PORT to crash on some systems.

PORT v0.8.5a-beta 03/08/2018

[config file]

• same as v0.8.4-beta

[bug fixes]

• correctly displays expected number of reads and path to summary file for "Gene Normalization" results in the .run_normalization.log file
• fixed bug which threw "Possible precedence issue with control flow operator" warnings when using perl versions >= 5.20

PORT v0.8.5-beta 01/02/2018

[config file]

• same as v0.8.4-beta

[news]

• gives warning when transcript and gene ids are the same in convert_gtf_to_PORT_geneinfo.transcripts.pl and run_normalization script
  • note added to about_cfg page

[bug fixes]

• correctly handles unique only cases in filter_sam_gnorm.pl and filter_sam.pl script
• correctly handles pipes “|” in chromosome names
• checks the min number of reads for determining memory for parseblastout step
• quants2spreadsheet_gnorm and make_final_spreadsheets steps request more mem for 100+ samples
• fixed bug in make_list_of_highexpressers.pl generating highly expressed exons
• MakeRumJunctionsFile.pm "got here" placement
• stats directory path issue with -alt_out option resolved
• non-unique genequants memory issue for high depth sample fixed

PORT v0.8.4-beta 03/15/2017

[config file]

• same as v0.8.3-beta

[news]

• rRNA_mm9.fa file now includes the ncbi rRNA sequnces.

[bug fixes]

• runblast bug fixed (deletes temp file in parseblastout step and checks se/pe before deleting fa files)
• requests more mem in parseblastout and filtersam steps for larger datasets.

PORT v0.8.3-beta 1/23/2017

• Config file has been updated
  • added HOST_NAME option for head node job submission.

• News
  • added head node job submission option (HOST_NAME in config)
  • intermediate files in gzip format
  • mitochondrial chromosome not filtered (highexp steps deals with highly expressed features).
  • performs intergenic region quantification and outputs spreadsheets (exon-intron-junction level).
  • requests more memory if jobs exit without error (restart_failedjobs_only.pl).
  • sam2genes step splits files into 5million lines in each temp file (2.5million when -norm option is used).
  • delete sam2genes temp files right after cat_genes_files step.
  • delete fasta and blastdb files generated in blast step immediately.
• Bug fixes
  • delete existing temp files before splitting files in sam2genes step.
  • queue update for large datasets (genefilter, run_shuf and make_final_spreadsheet step)
  • request more memory in filtersam step when # of ribosomal reads > 30mil.
  • ribopercents memory 10G -> 3G.
  • but fix in cat_highexp_files.pl
  • sam format check for the entire sam in filtersam step
  • print chromosome list discrepancy warning once.
  • create new STATS directory in PART1 when -alt_out option is used.

PORT v0.8.2a-beta 10/18/2016

• bug fixes
  • filtersam step needed more memory with >15,000,000 ribosomal ids.

PORT v0.8.2-beta 10/17/2016

• News
  • filter high expressers step runs much faster.
  • removed "gene:" from spreadsheets.
  • changed default reporting cutoff for high expressers to 3% (from 5%).
  • a new STATS directory is created when the '-alt_out' option is used (inside the -alt_out location).
  • aligner options for PORT compatibility provided for STAR and GSNAP (in README)
  • config file updated.
    • only takes one gene information file (GENE_INFO_FILE)
• Bug fixes
  • convert gtf to gene info script bug fix (header).
  • removed hap chromosomes from hg19_ensGenes.txt file.
  • blast option fixed.