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Reads were aligning to GRCm38 with HISAT2 (Kim D et al., 2015).
Everything is aligning to have VR hit critical mass next year.
Maybe this pole that I am aligning with is aligning to my younger self!
TopHat allows two mismatches when aligning to a reference genome.
Reads aligning to more than 10 genes are discarded.
A read aligning to all splice variant of a gene is counted once, and the reads uniquely aligning to various splice variants of a gene are pooled.
Reads aligning to non-proximal restriction sites were designated as "mispaired".
Oligonucleotides aligning to more than one gene and probes without perfect matches were excluded.
Only reads uniquely aligning to the genome with one mismatch were considered for further analysis.
Fusions without spanning pairs or breakpoints aligning to exon boundaries are discarded.
Reads aligning to exons were counted by HTSeq [ 43], using the "intersection-strict" mode.
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