Project description:We developed a software package STITCH (https://github.com/snijderlab/stitch) to perform template-based assembly of de novo peptide reads from antibody samples. As a test case we generated de novo peptide reads from protein G purified whole IgG from COVID-19 patients.

2022-07-21 | PXD031941 | Pride

Merging short and stranded long reads improves transcript assembly

Project description:New tools for improved long-read transcript assembly and coalescence with its short-read counterpart are required. Using our short- and long-read measurements from different cell lines with spiked-in standards, we systematically compared key parameters and biases in the read alignment and assembly of transcripts. We report a cDNA synthesis artifact in long-read datasets that impacts the identity and quantitation of assembled transcripts. We developed a computational pipeline to strand long-read cDNA libraries that markedly improves assembly of transcripts from long-reads. Incorporating stranded long-reads in a new hybrid assembly approach, we demonstrate its efficacy for improved characterization of challenging lncRNA transcripts. Our workflow can be applied to a wide range of transcriptomics datasets for superior demarcation of transcript ends and refined isoform structure, which can enable better differential gene expression analyses and molecular manipulations of transcripts.

2023-10-14 | GSE215357 | GEO

Merging short and stranded long reads improves transcript assembly

2023-10-14 | GSE215355 | GEO

Aegilops tauschii

Project description:Aegilops tauschii Raw sequence reads

| PRJNA705859 | ENA