Hi,
We recently did Fungal ITS paired-end sequencing using Illumina. It turns out that overall, the read 1s do not, whereas read 2s pass the sequence quality metrics. Before sequencing we had checked the quality of the DNA by running a gel, a nanodrop.and qubit. Can someone give us some hints as to why this might have happened?
Also, is it ok to use only the read 2s from this sequencing run and analyze it as a single end data?
Thanks for your help.
We recently did Fungal ITS paired-end sequencing using Illumina. It turns out that overall, the read 1s do not, whereas read 2s pass the sequence quality metrics. Before sequencing we had checked the quality of the DNA by running a gel, a nanodrop.and qubit. Can someone give us some hints as to why this might have happened?
Also, is it ok to use only the read 2s from this sequencing run and analyze it as a single end data?
Thanks for your help.
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