Use mudskipper to project HISAT2 genomic alignment onto transcriptome

[drpatelh]

Description of feature

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Bioconda

Currently, we don't have a native quantification method for HISAT2 genomic alignments because we need to project these onto transcriptomic alignments for accurate quantification with tools like Salmon. Using mudskipper gives us this option! 🎉

As a side, it will be interesting to compare the results from the 3 routes in the pipeline to see what the results look like!