pXg v2.4.1

Updates

• Added an option to select raw read count or normalized read count (i.e., RPHM, read-per-hundread-million). RPHM is the preferred choice when analyzing multiple BAM files, and it is set as the default.
• Added an option to print target-only results, which is useful for assigning read counts to confident peptides (e.g., those already verified by database search).
• Implemented a new function to build a database from FASTA files and pXg results. This functionality is available in "BuildSequenceDB.jar." The potential applications of this database are still being explored.

Full Changelog: v2.4.0-2024-12-10...v2.4.1-2025-03-13

pXg v2.4.0

Updates

• Some of parameter names were changed.
• "mode" parameter was changed to indicate strandedness.
  • Six-frame translation is used only for "none-strandedness."
  • In the paired-ends, it automatically determines the strandedness.
  • In the single-end, a user must specify a strandedness.
• Several columns were changed.
  • "InferredPeptide" presents not only the translated sequence but also the PTM annotation.
  • Length feature was introduced in PIN format
  • "MainScore" was changed to "Score" in PIN format

TODO

• Automatic determination of strandedness in a single-end dataset

Full Changelog: v2.3.2-2024-09-09...v2.4.0-2024-12-10

pXg v2.3.2

• Deal with "NULL" transcript or gene information in GTF file, particularly from Ensembl.

Full Changelog: v2.3.1-2024-07-29...v2.3.2-2024-09-09

pXg v2.3.1

• Report flank sequences, which are calculated by a frequency-based method.
• Do not report full RNA-seq sequences (unknown.seq) for unknown event of decoy matches.
• Do not write SAM file for decoy matches.
• Remove a debugging-purpose annotation in transcriptIDs column.

Full Changelog: v2.3.0-2024-05-15...v2.3.1-2024-07-29

pXg v2.3.0

• Now it can deal with multiple SAM/BAM files as input. Read count for each SAM/BAM file is written at the end of the column.
  The sum of reads from multiple SAM/BAM files is written in "Reads" column.
• To reduce memory usage, matched nucleotide sequences are indexed.

Full Changelog: https://github.com/HanyangBISLab/pXg/commits/v2.3.0-2024-05-15