I'm currently working on a RNA-seq dataset that isn't stranded, but when I load the bam files into IGV... and click on the "color alignments by strand", the majority of reads (even the ones mapped to introns) are color-coded in red or blue!
I'm not sure how it is determining which strand the read came from? How can IGV work out strand information out of nowhere, it seems?
Does anyone have a similar experience? What might be the reason?
I'm not sure how it is determining which strand the read came from? How can IGV work out strand information out of nowhere, it seems?
Does anyone have a similar experience? What might be the reason?
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