I am using SGSeq for alternative splicing analysis of the androgen receptor and was wondering if there was a way to tell the program only to use uniquely mapped reads from the BAM file in its analyses. As there seems to be discrepancy with IGV counting which I'd like to try to tease out.
You can influence which reads are analyzed when setting up the data frame with sample information. To do this column file_bam needs to be a BamFileList and sample information must be stored in a DataFrame object. Please see the manual page for Rsamtools::BamFileList for more details.