Question: Rna-Seq Library Design With Different Sequencing Depth
gravatar for clausndh
6.2 years ago by
European Union
clausndh50 wrote:

Hi Biostar Experts,

For the first time, I'm involved in designing a RNA-Seq experiment for a Illumina HiSeq-2000.
We have 16 samples which we have to divide at only 6 lanes! So is totally clear that we have to multiplex. And we can't use lane 7! or an additional flow cell.

My idea was to multiplex 4 lanes with 3 samples and 2 lanes with 2 samples. 1. Question: Is this a good design? 2. Question: With these design we will get samples with different sample sizes coming from the different sequencing depths. Do you think this a (big) problem for differential expression analyses?

My belief is that the normalizations form DESeq or edgeR are good enough to solve this problem.

Thank's for your help.

ADD COMMENTlink modified 6.2 years ago by support630 • written 6.2 years ago by clausndh50
gravatar for Devon Ryan
6.2 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

FYI, you have 16 samples, not probes (in case you're German, "Probe" in German is different from "probe" in English).

In an ideal world you'd just multiplex all the samples on each of the lanes (i.e., put all 16 samples on each of the lanes). Should that prove logistically difficult, your alternative proposal would be OK. DESeq/edgeR/etc. won't have much problem with that (I usually see people running into problems when the size factors differ by ~10x). BTW, depending on your goals, half to a third of a HiSeq lane per sample may be overkill (you can probably get away with 2-4 lanes for your samples, depending on the circumstances).

ADD COMMENTlink written 6.2 years ago by Devon Ryan94k
gravatar for support
6.2 years ago by
Austin, TX
support630 wrote:

If you evenly distribute your samples across 16 lanes, you should get around ~70M reads per sample. See this query on Genohub. If you're looking for differential expression the number of reads you're getting is probably overkill. Here are some recommended parameters.

I agree with the last answer that ideally you should barcode each of your libraries, pool them together and load equally in each lane.

-- Genohub

ADD COMMENTlink written 6.2 years ago by support630
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