Does anyone know what the best read length is to quantify splice variants from RNA seq data using an Illumina HiSeq. The reference genome has been sequenced so assembly is not too much of a problem.
On one hand the longest possible read length will increase identification of splice variants. However, with a shorter read length, more fragments can be sequenced (for a similar price), which increases quantification.
Is there such a thing as an optimal read length in this case?
Thanks for any input!
On one hand the longest possible read length will increase identification of splice variants. However, with a shorter read length, more fragments can be sequenced (for a similar price), which increases quantification.
Is there such a thing as an optimal read length in this case?
Thanks for any input!
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