Hi everybody,
I am currently planning a mRNA-seq experiment in a non-model species with the first goal being to study multiple copies elements expressed in the transcriptome.
TruSeq RNA sample preparation v2 Guide from Illumina suggests a 8min fragmentation step, which should give you a distribution of RNA fragment between 120bp to 210bp, with a median around 155bp.
However, as I am planning paired-end 100bp reads, it seems to me that I will loose some sequencing efforts (middle of inserts sequences twice).
- Have anyone tried to optimize fragmentation time as suggested on p.110 of this guide?
- What kind of fragmentation time have you used for paired-end reads?
Thanks!
Anne-Marie
I am currently planning a mRNA-seq experiment in a non-model species with the first goal being to study multiple copies elements expressed in the transcriptome.
TruSeq RNA sample preparation v2 Guide from Illumina suggests a 8min fragmentation step, which should give you a distribution of RNA fragment between 120bp to 210bp, with a median around 155bp.
However, as I am planning paired-end 100bp reads, it seems to me that I will loose some sequencing efforts (middle of inserts sequences twice).
- Have anyone tried to optimize fragmentation time as suggested on p.110 of this guide?
- What kind of fragmentation time have you used for paired-end reads?
Thanks!
Anne-Marie
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