using only uniquely-mapping reads for alternative splicing using SGSeq
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116100016 • 0
@116100016-22156
Last seen 22 months ago

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.

rna seq SGSeq Alternative splicing • 236 views
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@leonard-goldstein-6845
Last seen 12 months ago
United States

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.

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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.

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