PepQueryMHC v1.0.6

Updates

• Fix an issue in counting primary reads (now correctly excludes both secondary and supplementary reads).
• Correct typo: intron-retention → Intron-retention.

Full Changelog: v1.0.5...v1.0.6

PepQueryMHC v1.0.5

Updates

• Improve PTM parser.
• Fix some minor bugs.

Full Changelog: v1.0.4...v1.0.5

PepQueryMHC v1.0.4

Updates

• Keep the reference nucleotide sequence field empty when the peptide maps to unmapped reads.
• Support post-translational modification (PTM) annotations in input peptide sequences.
• Add an option to specify the sequence column name in target, scan, and fastq modes.
• Add options to specify the column names for location and strand in annotate mode.
• Implement automatic BAM indexing if the .bai index file is missing.
• Remove the .miss.tsv file; instead, unmatched peptides are now listed in each result file with a count of zero.
• Add a function to automatically detect strandedness for single-end data.
• Fix various minor bugs.

Full Changelog: v1.0.3...v1.0.4

PepQueryMHC v1.0.3

Updates

• Fix an exceptional case when summing reads across barcodes.
• Print abundant location and strand with its proportion in peptide output.

Full Changelog: v1.0.2...v1.0.3

PepQueryMHC v1.0.2a

Updates

• For clarity, EE is renamed to ASS (alternative splicing site).

Full Changelog: v1.0.2...v1.0.2a

PepQueryMHC v1.0.2

Changes in "annotate mode"

• Change class category
  • IF: In-frame in CDS (previous: PC, protein coding)
  • OOF: Out-of-frame in CDS (previous: FS, frameshift)
  • UTR: Untranslated region (previous: UTR)
  • ncRNA: Non-coding RNA (previous: ncRNA)
  • IR: Intron-retention (previous: IR)
  • asRNA: antisense RNA (previous asRNA)
  • IGR: Intergenic region (previous: IGR)
  • Unknown: Unknown region (previous: Unknown)
  • ES: Exon-skipping (previous: AS)
  • EE: Exon-exclusion (previous: AS)
• Change penalties and annotation rules
  • We introduce a concept of class to classify categories:
    • Class I: Exonic class such as IF, OOF, UTR, ncRNA
    • Class II: Intronic class, IR
    • Class III: Antisense class, asRNA
    • Class IV: Intergenic class, IGR
    • Class V: Exon-structural variations, EE, ES
    • Else: Unkown
  • Penalty of annotation is calculated by summing all maximum penalties in each class.
    • e.g., an annotation for UTR;IF;IR will be calculated max(UTR, IF) + max(IR).
  • Penalties:
    • IF: 0
    • UTR, FS: 20
    • ncRNA: 30
    • IR: 60
    • asRNA: 120
    • IGR: 240
    • Unknown: 480
    • Warning tag: 1000
    • ES: 15
    • EE: 15
  • Present a representative annotation
    • Annotation can stretch from UTR to OOF with ES and EE, leading to printing verbose annotation (e.g., UTR;OOF;ES;EE).
      To make it clean, worst priority annotation from Class I to Class IV is selected as the representative annotation. The example will be present "UTR;ES;EE".

Full Changelog: v1.0.1...v1.0.2

PepQueryMHC v1.0.1

Changes

• While reading the GTF file, transcripts tagged with cds_start_NF and cds_end_NF were previously ignored due to their ambiguous annotations. However, in cases where a gene contains only such transcripts, this led to a "null transcript" exception. To address this, these transcripts are now included in the warning column of the output, allowing users to review and handle them appropriately in annotation mode.
• If there is no provided location information or no matched reference name, these are annotated as "Unknown" with warning tags in annotation mode
• Null or irrelevant barcodes are excluded during single-cell RNA-seq processing. Reads associated with these barcodes do not contribute meaningful data and are therefore omitted from downstream analysis.

Full Changelog: v1.0.0...v1.0.1

PepQueryMHC v1.0.0

Initial release.

• Four modes are supported: scan/target/fastq/annotate mode.
• Scan and target modes support multi-threading.