Question: using only uniquely-mapping reads for alternative splicing using SGSeq
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gravatar for 116100016
7 weeks ago by
1161000160
1161000160 wrote:

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.

ADD COMMENTlink modified 7 weeks ago by Leonard Goldstein110 • written 7 weeks ago by 1161000160
Answer: using only uniquely-mapping reads for alternative splicing using SGSeq
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gravatar for Leonard Goldstein
7 weeks ago by
United States
Leonard Goldstein110 wrote:

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.

ADD COMMENTlink written 7 weeks ago by Leonard Goldstein110

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.

ADD REPLYlink written 7 weeks ago by Leonard Goldstein110
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