New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Develop 2 month plan process Hawaii Oyster Samples #962
Comments
bulk of the samples we have from Hawaii |
Is there a data sheet associated with samples Ronit worked with? |
lets do some deep triploid v diploid comparisons |
Also have triploid C.gigas (n = 4) from Nisbet Oyster Co. Collected ctenidia, gonad, mantle, muscle from each. |
@kubu4 what would be the cost for 10 samples RNA-seq and when would they have to be submitted to be billed by end of August? Same for Bisulfite Seq (presuming WGBS which would require deeper coverage)? |
Does it matter where we submit? |
Sorry, I should have phrased it: Can we submit them anywhere? |
Also, what type of sequencing depth are we looking at for the BSseq? |
Anywhere is fine, maybe run a couple of options, one being UW.
…On Jul 1, 2020, 6:00 AM -0700, kubu4 ***@***.***>, wrote:
Sorry, I should have phrased it: Can we submit them anywhere?
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub, or unsubscribe.
|
Not quite sure, - can see if what recommendation might be. Wild guess is 100x
Also worth getting idea if we did do MBD-BS (less coverage) with 20x probably sufficing.
Yaamini’s recent paper can provide good estimate for MBD-BS coverage
…On Jul 1, 2020, 6:06 AM -0700, kubu4 ***@***.***>, wrote:
Also, what type of sequencing depth are we looking at for the BSseq?
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub, or unsubscribe.
|
Genewiz quotes (guaranteed <20 business days). Outputs listed below are based on Genewiz's recommendation based on genome size. RNAseq (20 - 30M reads; 150bp PE; stranded):
WGBS (>30x coverage; 150bp PE):
EDITED: Added note about Genewiz recs. |
NWGC (UW) can bill by the end of August if we submit samples no later than July 20, 2020. RNAseq (~30M reads):
|
Now, just waiting on ZymoResearch. Should have a call today with a project manager. |
ZymoResearch quotes: RNAseq (30M reads; 150bp PE; stranded):
Waiting on them to update WGBS quote, due an oversight on their end. |
ZymoResearch quote: WGBS (>30x coverage; 150bp PE):
|
I should add that I think that Zymo WGBS quote is calculated incorrectly (I think it is for far greater than 30x coverage). I've sent a message to them to double-check the math. |
Alrighty, updated quote from Zymo: WGBS (>30x coverage; 150bp PE):
|
Regarding ploidy and epigenetics
The text was updated successfully, but these errors were encountered: