Hello,
I've mapped some reads with tophat using "fr-firststrand" option. I'm on single read, I excepected all my reads will be in the same strand but viewing my .bam file with IGV it looks like I got reads both orientation on my reads : http://imgur.com/GKCLibr (ie arrow are not in the same direction)
How is that possible ? Does that make sence ?
I've mapped some reads with tophat using "fr-firststrand" option. I'm on single read, I excepected all my reads will be in the same strand but viewing my .bam file with IGV it looks like I got reads both orientation on my reads : http://imgur.com/GKCLibr (ie arrow are not in the same direction)
How is that possible ? Does that make sence ?
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