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Posts by sandersonrbt
... I believe the option you would want there is --outReadsUnmapped Fastx. This will make a separate file of all the unmapped reads, albeit in fasta/fastq format (which you could potentially check for fusions using different tools/parameters). I am not sure how useful a BAM file of unaligned reads would ...
... In general, I use and recommend others use STAR with the default settings unless there is a specific reason to change them. In my experience many options are great for fine-tuning your analysis to suit the particulars of your sequencing runs (trying to account for low depth/short-reads/etc) but I ra ...
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