Sorry if this is a silly question.
Assuming here mapped ~ aligned.
My understanding is that TopHat output contains only alignment information. Therefore, not all input reads make it into the output, because not all reads align.
Can I conclude that because the unmapped reads don't make it in the Tophat output, the flagstat tools will always return 100% of reads mapped on a tophat output?
Assuming here mapped ~ aligned.
My understanding is that TopHat output contains only alignment information. Therefore, not all input reads make it into the output, because not all reads align.
Can I conclude that because the unmapped reads don't make it in the Tophat output, the flagstat tools will always return 100% of reads mapped on a tophat output?
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