Hey there,
I'm interested in analyzing transcriptome-wide differential gene expression in zebrafish (1.7Gb genome) under three conditions (inc. control). Each condition is a pooled sample of RNA from 3-5 fish.
Can anyone provide a strategy to determine if I can multiplex all three conditions and still maintain some statistical strength?
My local sequencing lab can combine up to 92 samples in one lane, "as long as the yield is sufficient for [my] research".
Their current yield is 100-200M clusters/lane, prior to quality filtering.
I'm interested in a basic transcriptome analysis (no SNP or isoform detection necessary).
Unfortunately, I'm still waiting to hear back from the sequencing lab whether they use v2 or v3 chemistry, but it would be greatly appreciated if you have any advice in the meantime. Cheers.
I'm interested in analyzing transcriptome-wide differential gene expression in zebrafish (1.7Gb genome) under three conditions (inc. control). Each condition is a pooled sample of RNA from 3-5 fish.
Can anyone provide a strategy to determine if I can multiplex all three conditions and still maintain some statistical strength?
My local sequencing lab can combine up to 92 samples in one lane, "as long as the yield is sufficient for [my] research".
Their current yield is 100-200M clusters/lane, prior to quality filtering.
I'm interested in a basic transcriptome analysis (no SNP or isoform detection necessary).
Unfortunately, I'm still waiting to hear back from the sequencing lab whether they use v2 or v3 chemistry, but it would be greatly appreciated if you have any advice in the meantime. Cheers.