Has anyone compared RNA-seq data generated on a SOLiD v3/v4 with a 5500 -- for the same sample ?
We've recently taken the same total RNA sample, constructed a 5500 library and performed a 50bp run on it. A comparison of the data (v4 vs. 5500), looks considerably different. On it's own -- the 5500 data looks great ! But the correlation between the two data sets is very poor. A handful of qPCR expression assays -- tends to confirm the 5500 data.
Does anyone have any experience with this ? Several changes have taken place with the 5500 upgrade -- new library construction protocol ("T/A" tailed ligation, bead clean-ups, etc.), updated 5500 chemistry, new instrument,etc.
One would expect higher quality data -- and more of it. What's disconcerting is how different it looks from the v4 data.
Any ideas would be greatly appreciated !
Thanks,
Michael
We've recently taken the same total RNA sample, constructed a 5500 library and performed a 50bp run on it. A comparison of the data (v4 vs. 5500), looks considerably different. On it's own -- the 5500 data looks great ! But the correlation between the two data sets is very poor. A handful of qPCR expression assays -- tends to confirm the 5500 data.
Does anyone have any experience with this ? Several changes have taken place with the 5500 upgrade -- new library construction protocol ("T/A" tailed ligation, bead clean-ups, etc.), updated 5500 chemistry, new instrument,etc.
One would expect higher quality data -- and more of it. What's disconcerting is how different it looks from the v4 data.
Any ideas would be greatly appreciated !
Thanks,
Michael
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