https://github.com/bzhanglab/pepquerymhc - 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: https://github.com/bzhanglab/PepQueryMHC/compare/v1.0.3...v1.0.4

- Java
Published by progistar 12 months ago

https://github.com/bzhanglab/pepquerymhc - 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: https://github.com/bzhanglab/PepQueryMHC/compare/v1.0.2...v1.0.3

- Java
Published by progistar about 1 year ago

https://github.com/bzhanglab/pepquerymhc - PepQueryMHC v1.0.2a

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

Full Changelog: https://github.com/bzhanglab/PepQueryMHC/compare/v1.0.2...v1.0.2a

- Java
Published by progistar about 1 year ago

https://github.com/bzhanglab/pepquerymhc - 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: https://github.com/bzhanglab/PepQueryMHC/compare/v1.0.1...v1.0.2

- Java
Published by progistar about 1 year ago

https://github.com/bzhanglab/pepquerymhc - PepQueryMHC v1.0.1

Changes * While reading the GTF file, transcripts tagged with cdsstartNF and cdsendNF 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. * 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: https://github.com/bzhanglab/PepQueryMHC/compare/v1.0.0...v1.0.1

- Java
Published by progistar about 1 year ago

https://github.com/bzhanglab/pepquerymhc - PepQueryMHC v1.0.0

Initial release.

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

- Java
Published by progistar over 1 year ago