Hi, I am using STAR to align my illumina reads to a reference. For a multimapped read that maps equally well to multiple locations, should I
- keep all alignments for multiple locations
- keep one alignment (one location, primary alignment) and discard all other alignments (secondary alignments)
- remove all alignments (primary and secondary alignments) for all locations
Which is better (1,2,3) for differential expression analysis [FEATURECOUNTS+DESEQ2] and differential isoform analysis [RSEM]? Should I filter first by MAPQ and then by primary alignment? Also how does one filter a BAM file for primary alignments?
Is it better to change some setting with the aligner during mapping or with the DGE tool?