2020年3月12日 · The primers are actually are not used in the default profile HMM mode. The "universal tags" are used for PCR, but these primers are based on the reverse transcription and strand switching primers.

Pychopper v2 is a tool to identify, orient and trim full-length Nanopore cDNA reads. The tool is also able to rescue fused reads. The general approach of Pychopper v2 is the following: Pychopper first identifies alignment hits of the primers across the length of the sequence.

A tool to identify, orient, trim and rescue full length cDNA reads - nanoporetech/pychopper

2024年2月22日 · A pool of 1–100 primers can be used and should target 30 nt downstream of the BSJ or downstream of the 5′ end of a conserved exon among different isoforms obtained from the same circRNA host gene. The second strand of the cDNA is synthesized using a matching pool of back-to-back and divergent primers (Fig. 2).

2021年8月10日 · The need for gene-specific primers makes this technique ideal for delineating the complexity of circRNAs identified in global screens, from circRNA databases or computational predictions for a ...

2023年9月21日 · Here we describe a streamlined method to analyse mRNA vaccines and therapies using long-read nanopore sequencing. Compared to other industry-standard techniques, VAX-seq can comprehensively measure...

Full-length cDNA reads containing strand-switching primer (SSP) and anchored oligo (dT) VN primer (VNP) in the correct orientation were identified using Pychopper (v.2.5.0) with standard parameters using the default pHMM backend and autotuned cutoff parameters estimated from subsampled data (github.com/nanoporetech/pychopper).

Full-length cDNA reads containing SSP and VNP primers in the correct orientation were identified using pychopper (v.2.5.0) with standard parameters using the default pHMM backend and autotuned cutoff parameters estimated from subsampled data

2022年10月20日 · Second round full-length cDNA reads identification applied to the unclassified direct cDNA reads with DCS-specific read rescue enabled (parameter -x). DCS109 can suffer from a specific reverse transcription artefact, which will lead to 2D-like reads with two VNP primers at the ends.

2023年2月3日 · Plasmid pRSFDuet-1_VNp-LZ_VNp-LZ-hGH from Dr. Dan Mulvihill's lab contains the inserts VNp-LZ-hGH and VNp-LZ and is published in Cell Rep Methods. 2023 Feb 2;3 (2):100396. doi: 10.1016/j.crmeth.2023.100396. eCollection 2023 Feb 27. This plasmid is available through Addgene.