This was found to be particularly relevant to excluding blast-homology detection between BRAF and AKAP9 in gencode v31 where additional transcript annotations in both genes extend into Alu elements and would otherwise be detected as false homology. Because of repbase licensing requirements, its more straightforward to just use Dfam with nhmmer for identifying human-homologous repeat elements and softmask them prior to blast. (this is similar to the earlier repeatmasker approach used in earlier versions of STAR-Fusion. use Dfam-based masking of cds-plus database prior to blast & homology detection. allow exceptions to requirement of breakpoint-defining reads such as IGH-CRLF2 where breakpoints may be ill defined given complex structural rearrangements. bugfix for RT-artifact removal, no longer case sensitive on splice dinucleotides
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