Tophat2 Aligning extremely short reads
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3.3 years ago
biogirl04 ▴ 10

Hi,

Can tophat2 align reads with lengths = 6bp? If not, which tool can?

Thanks!

RNA-Seq Tophat alignment sequencing • 592 views
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I do not see how any alignment of a hexamer would be meaningful. Simply because of the stochastic reasons, any hexamer would have a large amouts of occurrences in the genome. What exactly are you trying to do any why?

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Maybe you should look at blast , i don't think you are interest into spliced alignment with 6 read length ....

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