[Cv19caingest] Re: h5 files [EXT]

Hi Erin, It is an AnnData object that requires python package scanpy/anndata (https://scanpy.readthedocs.io/) to load. For conversion to Seurat object, you could try sceasy (https://github.com/cellgeni/sceasy). Many thanks, Ni ________________________________ From: Reichenberger, Erin R <REICHENBEE(a)chop.edu> Sent: Thursday, March 18, 2021 2:26:08 PM To: cv19caingest(a)sanger.ac.uk Subject: [Cv19caingest] Re: h5 files [EXT] 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