maximilianh
commented
3 years ago Oh! Semicolons in IDs, that's unusual. R doesn't allow this as far as I know so there is code that "cleans" the IDs. Do you think you can share the matrix and meta.tsv with me @.*** ? That would be easiest, otherwise I can dig into the code and look for the replace where the "cleaning" of the meta IDs happens...
On Sun, Sep 12, 2021 at 8:30 PM Daniel Vera @.***> wrote:
I had semicolons in my cell names and the vast majority of cells are removed because they did not "appear" in the metadata
@.***:~/creighton_wt$ sudo cbBuild -o /tmp/cb -p 80 INFO:root:dataRoot is not set in ~/.cellbrowser.conf or via $CBDATAROOT. Dataset hierarchies are not supported. INFO:root:Determining if /tmp/cb/creighton_wt/exprMatrix.tsv.gz needs to be created INFO:root:Reading headers from file /tmp/cb/creighton_wt/exprMatrix.tsv.gz INFO:root:current input matrix looks identical to previously processed matrix, same file size, same sample names INFO:root:/tmp/cb/creighton_wt/meta.tsv has the same md5 as in /tmp/cb/creighton_wt/dataset.json, no need to rebuild meta data INFO:root:Reading sample names from /tmp/cb/creighton_wt/meta.tsv INFO:root:Checking and reordering meta data to /tmp/cb/creighton_wt/meta.tsv INFO:root:Reading sample names from /home/ubuntu/creighton_wt/meta.tsv INFO:root:Reading headers from file /home/ubuntu/creighton_wt/exprMatrix.tsv.gz WARNING:root:14576 sample names are in the expression matrix, but not in the meta data. Examples: ['wta;TATCGCCGTCGAACGA-1', 'wtb;GTTGAACAGACGCATG-1', 'wta;GGCACGTCACAACGCC-1', 'wta;GTTTGGACACATTC TT-1', 'wtb;AGGTCTACAGCCTTCT-1', 'wtb;CTACTATGTAGATTGA-1', 'wtb;GTCAAGTCATCGATGT-1', 'wta;TCGTAGACATCGGCCA-1', 'wta;TTCCTAATCTGGCCTT-1', 'wtb;TCAGCCTCAGTTAGAA-1'] WARNING:root:These samples will be removed from the expression matrix, if possible INFO:root:Data contains 6 samples/cells [...]
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matthewspeir
I had semicolons in my cell names and the vast majority of cells are removed because they did not "appear" in the metadata
ubuntu@ip-172-31-24-90:~/creighton_wt$ sudo cbBuild -o /tmp/cb -p 80 INFO:root:dataRoot is not set in ~/.cellbrowser.conf or via $CBDATAROOT. Dataset hierarchies are not supported. INFO:root:Determining if /tmp/cb/creighton_wt/exprMatrix.tsv.gz needs to be created INFO:root:Reading headers from file /tmp/cb/creighton_wt/exprMatrix.tsv.gz INFO:root:current input matrix looks identical to previously processed matrix, same file size, same sample names INFO:root:/tmp/cb/creighton_wt/meta.tsv has the same md5 as in /tmp/cb/creighton_wt/dataset.json, no need to rebuild meta data INFO:root:Reading sample names from /tmp/cb/creighton_wt/meta.tsv INFO:root:Checking and reordering meta data to /tmp/cb/creighton_wt/meta.tsv INFO:root:Reading sample names from /home/ubuntu/creighton_wt/meta.tsv INFO:root:Reading headers from file /home/ubuntu/creighton_wt/exprMatrix.tsv.gz WARNING:root:14576 sample names are in the expression matrix, but not in the meta data. Examples: ['wta;TATCGCCGTCGAACGA-1', 'wtb;GTTGAACAGACGCATG-1', 'wta;GGCACGTCACAACGCC-1', 'wta;GTTTGGACACATTC TT-1', 'wtb;AGGTCTACAGCCTTCT-1', 'wtb;CTACTATGTAGATTGA-1', 'wtb;GTCAAGTCATCGATGT-1', 'wta;TCGTAGACATCGGCCA-1', 'wta;TTCCTAATCTGGCCTT-1', 'wtb;TCAGCCTCAGTTAGAA-1'] WARNING:root:These samples will be removed from the expression matrix, if possible INFO:root:Data contains 6 samples/cells[...]