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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.
Actually looking at the code in more detail, BamFile details from the sample information currently do not propagate. The hard-coded behavior is that only primary alignments in the BAM file are considered for analysis. In other words, each read should be analyzed only once, but the analysis may include reads that do not align uniquely. For your question it may be easiest to pre-filter BAMs to only contain uniquely mapped reads.