Feb 07, 2024
Differential transcript usage analysis
- 1University of Oxford
Protocol Citation: Peter Kilfeather 2024. Differential transcript usage analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.261gedmjdv47/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: February 07, 2024
Last Modified: February 07, 2024
Protocol Integer ID: 94806
Funders Acknowledgement:
Aligning Science Across Parkinson's
Grant ID: ASAP-020370
Monument Trust Discovery Award from Parkinson’s UK
Grant ID: J-1403
Abstract
Differential transcript usage analysis from Kilfeather, Khoo et al., 2024
Protocol
Protocol
Differential transcript usage was performed using DRIMSeq (v1.24.0). To consider only genes containing more than 1 isoform, with a minimum level of expression, the following parameters were used: min_samps_gene_expr = n * 0.75, min_gene_expr = 10, min_samps_feature_expr = 10, min_feature_expr = 10, min_samps_feature_prop = 10, min_feature_prop = 0.1.