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Swarbricklab-code / BrCa_cell_atlas

Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".
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About the "filtered_count_matrices.tar.gz" download on zenodo #19

Closed lhyNB closed 2 years ago

lhyNB commented 2 years ago

Hi, i am willing to know why there is an error like "the compressed file format is unknown or the contents are corrupted" when i unzip the file. When i unzip the other files download from the Zenodo, everything went well, however. Is there a problem with the uploaded file and could you please send me the latest file "filtered_count_matrices.tar.gz" that can be unzipped？Here is my email address 22119069@zju.edu.cn. Thank u. Wish u have a good day.

johnyaku commented 2 years ago

I just downloaded and tested the file. Extracted OK for me with tar -xvzf filtered_count_matrices.tar.gz. Perhaps the file was corrupted during transfer? You can check the md5 checksum by running md5sum filtered_count_matrices.tar.gz on the downloaded file. The result should match the md5 checksum displayed under the filename on Zenodo.

Once you manage to extract the tarball, you will find folders for each sample. Note that the actual matrices inside the archive (such as filtered_count_matrices/1142243F_filtered_count_matrix/matrix.mtx.gz) are not actually gzipped files, despite the .gz extension. You can either compress them or use them as is, depending on your downstream application.

In case you need to load these count matrices into Seurat, please check the following discussion: https://github.com/Swarbricklab-code/BrCa_cell_atlas/issues/3

lhyNB commented 2 years ago

I see…I tried again and it works. Thanks