Hi all friends,
I know that the high abundant transcripts are better assembled and represented by longer k-mer and shorter k-mer is suitable for reconstructing the low abundant transcript, but I'm not sure about the exact reason of it. Could you please explain to me why?
Thanks a lot
1 answer
Having a high quantity of expression, i.e high abundance of transcript, it could be possible to assembly them using a long k-mer instead of a shorter one. I mean, the basic idea about the k-mers is:
The shorter k-mer, the bigger sensitivity but smaller specificity: you will be able to assembly more reads (kmers) together but with larger error rate (i.e. you will assembly k-mers together that are not true).
Sohaving a high amount of data, you have more chance to assembly the correct kmers together and you could specify larger k-mers in order to reduce the error rate.
I hope you find this information useful.
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