Mar 15, 2024

Public workspaceIso-Seq mapping to L1HS/PA2 consensus sequence

DOI
dx.doi.org/10.17504/protocols.io.5qpvorw7dv4o/v1
  • 1Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden.
Raquel Garza
Open access
DOI: dx.doi.org/10.17504/protocols.io.5qpvorw7dv4o/v1
Protocol Citation: Raquel Garza 2024. Iso-Seq mapping to L1HS/PA2 consensus sequence. protocols.io https://dx.doi.org/10.17504/protocols.io.5qpvorw7dv4o/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: March 03, 2023
Last Modified: May 31, 2024
Protocol Integer ID: 78064
Keywords: ASAPCRN
Funders Acknowledgement:
Aligning Science Across Parkinson's through the Michael J. Fox Foundation for Parkinson's Research
Grant ID: ASAP-000520
Swedish Research Council
Grant ID: 2018-02694
Swedish Brain Foundation
Grant ID: FO2019-0098
Cancerfonden
Grant ID: 190326
Barncancerfonden
Grant ID: PR2017-0053
NIHR Cambridge Biomedical Research Centre
Grant ID: NIHR203312
Swedish Society for Medical Research
Grant ID: S19-0100
National Institutes of Health
Grant ID: HG002385
Swedish Research Council
Grant ID: 2021-03494
Swedish Research Council
Grant ID: 2020-01660
Abstract
The protocol describes the steps to map HiFi reads to a consensus sequence and retrieve density plots
Mapping to L1HS/PA2 consensus sequence
Mapping to L1HS/PA2 consensus sequence
A L1HS and L1PA2 consensus sequence was used to create a minimap2 (version 2.24; RRID:SCR_018550) index
Command
L1 consensus index minimap2
minimap2 -d L1consensus.mmi L1consensus.fa
to map FLNC reads (HiFi reads).
The density of mapped reads was visualized in the Integrative Genomics Viewer (IgV) (version 2.12.3; RRID:SCR_011793)
The number of mapped reads in the L1s 5’ UTR was retrieved using samtools view (-c) (version 1.9; RRID:SCR_002105), specifying the first 900 bp of the consensus sequence as the coordinates of interest.