Can someone suggest software/pipelines for analysis of alternative #splicing from long-read #RNAseq (from #Nanopore #MinION)? Basically, I'd like to quantify abundance of different splicing variants in different samples. #bioinformatics
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@nicolaromano You can try StringTie2 (https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual) and FLAIR (https://flair.readthedocs.io/en/latest/) to discover transcript isoforms from all samples and quantify them with packages like featureCounts (https://subread.sourceforge.net/) and Salmon (https://salmon.readthedocs.io/en/latest/salmon.html)
@applepie Thank you! Much appreciated, I'll have a go at those!