Greetings,
Thank you for making the data available for download. I have downloaded some data (https://covid19.cog.sanger.ac.uk/submissions/release1/20200804_NasalSwab_Br…), however I have been unable to open it
I get errors like this:
Warning: Unknown file type: h5ad
Warning: 'assay' not set, setting to 'RNA'
Creating h5Seurat file for version 3.1.5.9900
Adding X as data
Adding X as counts
Error: Cannot find feature names in this H5AD file
Execution halted
Or this:
error #001: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Dio.c in H5D__read(): line 551: can't read data
class: HDF5
major: Dataset
minor: Read failed
error #002: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Dchunk.c in H5D__chunk_read(): line 1875: unable to read raw data chunk
class: HDF5
major: Low-level I/O
minor: Read failed
error #003: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Dchunk.c in H5D__chunk_lock(): line 2905: data pipeline read failed
class: HDF5
major: Data filters
minor: Filter operation failed
error #004: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Z.c in H5Z_pipeline(): line 1347: required filter 'lzf' is not registered
class: HDF5
major: Data filters
minor: Read failed
There are many message boards that have listed possible solutions, but I have not been able to get any of them to work. Could you provide some guidance as to what programs are used to open/manipulate these files please?
Sincerely,
Erin
Hi,
I previously contributed data to the COVID-19 Cell Atlas. I now have an updated/finalized Fetal Cerebellum dataset that I would like to replace for the dataset that is currently hosted: https://www.covid19cellatlas.org/index.healthy.html
What is the best way to transfer the updated .rds?
Thanks!
Kimberly A Aldinger, PhD (she/her)
Center for Integrative Brain Research (CIBR)
Seattle Children's Research Institute
Member, Brotman Baty Institute for Precision Medicine
206-884-1226 OFFICE
206-884-1210 FAX
OFFICE Center for Integrative Brain Research, Seattle Children's Research Institute, 1900 9th Avenue, Seattle, WA 98101
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Hi Ni and COVID-19 Cell Atlas Team,
I hope you are doing well. I'm writing to request some guidance on updating
our group's previous submission to the COVID-19 Cell Atlas Portal (current
data and viewer is "Nasal Epithelia":
https://urldefense.proofpoint.com/v2/url?u=https-3A__cellxgene.cziscience.c…
)
We just submitted our manuscript and are in the process of uploading this
manuscript as a preprint to biorxiv. We would love to supply the data link
for the expanded and updated object. How would you like us to proceed? I
can provide an updated h5ad, though I had some difficulties in formatting
this properly before (I generally work in R/Seurat).
Thanks in advance!
Carly
--
Carly G. K. Ziegler
Harvard/MIT MD-PhD Program
Carly_Ziegler(a)hms.harvard.edu
carly.ziegler(a)gmail.com
404-375-8912
Dear friend,
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Hello,
I am having trouble downloading single cell expression data from your website. After following the download link below,
https://covid19.cog.sanger.ac.uk/byrd20_gingiva.processed.h5ad
I am brought to a page stating:
AccessDeniedcovid19tx0000000000000145d590a-00601c602e-2b1cd989-default2b1cd989-default-default
Could you recommend a solution for me?
Thank you in advance,
Sawyer Hicks
Berglund Lab
PhD Student
Good Morning,
If it is possible, we would like to upload our COVID-19 patient data to the COVID-19 Cell Atlas web portal.
Please let us know how we can begin this process. The data is currently unpublished.
Many thanks and best wishes,
Emily
Emily Stephenson
Haniffa Lab
M3.121 Leech Building
Faculty of Medical Sciences
Newcastle University
NE2 4HH
Happy New Year
Hi, Dear Dr. Sungnak and Covid-cell Atlas
I wonder if I could get access to this precious data and I am interested with ACE2 and other gene expressed in kidney epithelial cells.
Many thanks!
Happy New Year!
Dungeng
Dear all,
We, computational scientists, are developing new statistical methods for the analysis of single-cell data. The application of these methods to COVID-19 data has revealed novel findings in terms of its biology, which would also impact its treatment. We are gearing towards the submission of these findings. Could you let us know regarding the policy of publication manuscripts that leverage COVID19 cell atlas data? We will be happy to accommodate researchers who had generated the data as co-authors in the manuscript as deemed necessary.
Avinash Sahu
Research Fellow
asahu(a)ds.dfci.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__connects.catalyst.harv…
Hello,
I had a question about the pre-processing of the datasets hosted on the covid19cellatlas.org<http://covid19cellatlas.org>. I am sorry if I reached out on a wrong address, and I would be grateful if you could forward me to the right person.
Specifically, I am interested in the information on the normalization/processing of the raw expression values, used to generate the .h5ad files for the healthy donors. I noted on the data ingestion information that the raw counts are always pre-processed, but no information on what that processing is or for what datasets that affected. So, I would be grateful if you could clarify this.
Sincerely yours,
Ksenia Sokolova
