Cv19caingest March 2021

cv19caingest@sanger.ac.uk

3 participants
3 discussions

Blish lab: New single-cell dataset for COVID-19 cell atlas [EXT]

by Aaron James Wilk

Hi there, My name is Aaron Wilk from the Blish lab at Stanford University. Your cell atlas is currently hosting our early COVID-19 scRNA-seq immune profiling work, and I am excited to tell you that we have now posted a preprint expanding that initial work to many more patients across a wider range of disease severity: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_conten… Would you be able to host Seurat .rds and .h5ad for this dataset as well? Please let me know if you have any questions. All the best, Aaron Wilk

2 years, 10 months

Re: h5 files [EXT]

by Reichenberger, Erin R

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

3 years, 1 month

updated dataset for COVID-19 Cell Atlas [EXT]

by Aldinger, Kimberly

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 MAIL 1900 9th Avenue, M/S JMB-10, Seattle, WA 98101 WWW https://urldefense.proofpoint.com/v2/url?u=https-3A__www.seattlechildrens.o… CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

3 years, 1 month

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Cv19caingest March 2021