Comments (16)
I appreciate your support!
Kind Regards,
Hyun-Hwan Jeong
from crispulator.jl.
Could you clarify what you mean by the count matrix?
from crispulator.jl.
Oh sorry, I would explain it clearly. Crispulator simulates the deep sequencing, and we can have read numbers of each sgRNA for low/high reporter bin. I want to have the read numbers once I run the tool, and I called it count matrix because we can have the sgRNA read numbers for each bin with the form of n x 2 matrix (n is the number of sgRNA, and columns are for low/high bin). I hope I clarify it well.
Thank you
from crispulator.jl.
Sorry for not getting back to you sooner. Crispulator does generate your count matrix, but doesn't export it currently. It should be relatively easy to add.
from crispulator.jl.
Hello @tlnagy,
I recently realized that you provide the bc_counts
data frame, and it stores counts of each sgRNA from the high-throughput sequencing. Therefore, I think you don't have to add any additional function or script. Please correct me if I am wrong or close this issue if it is otherwise. I thank you for your attention to this request and I congratulate your recent publication of this great tool in the journal!
Thank you,
from crispulator.jl.
Let me know if bc_counts
worked for you! If not, please open a new issue. I'm going to add an example to the docs based on your example in #52. I think it would help others in the future!
from crispulator.jl.
I think it is a kind of okay if I want to build single counts for each group. However, I'd like to have any idea how to build the matrix under below conditions:
- Generate another
bc_counts
of un/pre-sorted cells with keeping counts of the high and low. - Generate multiple replicates under the same configuration, I did it before, but not 100% sure my method is correct.
Thank you,
Hyun-Hwan Jeong
from crispulator.jl.
Generate another bc_counts of un/pre-sorted cells with keeping counts of the high and low.
Are you simulating a FACS Screen?
from crispulator.jl.
Are you simulating a FACS Screen?
Yes, for the case.
from crispulator.jl.
Generate another bc_counts of un/pre-sorted cells with keeping counts of the high and low.
I realized that obs_phenotype
was supposed to serve this purpose so I reverted the previous commit that deleted it. I fleshed out the docs further. http://tamasnagy.com/Crispulator.jl/latest/custom.html#Performing-the-screen-1 should help you with getting the observed phenotype, i.e. the phenotype on which the cells were sorted with FACS
EDIT: It sounds like you obs_phenotype
for each individual cell, not on a per-guide level basis, correct?
I think that would involve exporting observed
:
Crispulator.jl/src/simulation/selection.jl
Lines 20 to 22 in 46a804c
from crispulator.jl.
Hello @tlnagy,
Thanks for your reply, but I do not want to have cell count, and my language made you confused. My question must be corrected as "Can we have read counts for sgRNA for [0,100%] bin or [25%,75%] bin?". I wanted to simulate a CRISPRn experiment like 1. In Figure 1 of the [1], you can see they collected and sequenced for "unsorted cells". Hope it makes you clear now.
Thank you and Best,
Hyun-Hwan Jeong
from crispulator.jl.
I see what you want. So I've had to rearchitect differences_between_bins
to support this approach. It's almost ready. I'll push a PR once I'm done.
from crispulator.jl.
Hey @hyunhwaj, if you get a chance can you check out the notebook in #53? It has the Unsorted, GFP_low, GFP_high bins that you were looking for. Let me know over there if it works for you.
You should be able to check it out using
git fetch origin pull/53/head:add-multibin-support
git checkout add-multibin-support
in the Crispulator directory
from crispulator.jl.
I merged #53 into master so now you should be able to run
Pkg.checkout("Crispulator")
to give it a spin. Please open a new issue if you run into any issues or have suggestions!
from crispulator.jl.
That's actually what I've wanted! I checked the notebook, and this ran without any problem. I truly appreciate your work.
Hyun-Hwan Jeong
from crispulator.jl.
Thanks! Let me know if you need anything else.
from crispulator.jl.
Related Issues (20)
- Performance of analysis code has degraded HOT 3
- Restructure library.jl
- Test simulation on Windows
- Plotting on 32-bit windows is broken
- Current design crashes with latest stats packages HOT 4
- Modularize and add integration tests
- Build out documentation HOT 1
- Things remaining to do for slim crispulator
- error on `exp` mode HOT 1
- Error tagging new release
- "run.jl config" is not working HOT 4
- "-Inf" values of obs_phenotype HOT 5
- Add Julia 1.0 support
- Info about upcoming removal of packages in the General registry HOT 1
- TagBot trigger issue HOT 4
- Improve flexibility of screen design
- Consolidate cells and guides
- Non-zero WT behavior subtly breaks guide quality model
- Added functionalities and saving raw table
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