Welcome to CeleScope Discussions! #27
Replies: 6 comments 18 replies
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Hi, I use Telescope to analyze single cell RNA data generated by Singleron. -- celescope.tools.step.get_slot_key - WARNING - Assay not found in sample_summary.metrics i think its related with the --sample Attribute. thanks! |
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Hi, I'm kind of new to bioinformatics and I wanted to try out CeleScope according to the user guide. |
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Hi, How to install it on public HPC system, with no conda command available? |
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Hi, I was looking for information about index files, I got for each sample in context to scRNAseq. Do I need to provide this as an input somewhere? I could not find this info here https://github.com/singleron-RD/CeleScope/blob/master/doc/assay/multi_rna.md |
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Where can I find the complete documentation for Celescope? I've received the final report, which includes two folders in the output—'raw' and 'filtered.' I'm unsure about which input to use for Seurat (raw or filtered). I couldn't find any documentation that explains the output details comprehensively, including the default filters applied. Additionally, I'm curious about the tool or method Celescope uses for clustering cell types. When I use filtered data as input in Seurat, I observe different clusters than those generated by Celescope. Can you provide insights into this discrepancy?" |
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I am running some DynaSCOPE samples and I wanted to get familiar with the celescope analysis. I first downloaded and installed the conda packages like on this site Then I downloaded all the data and scripts like this
Then I generated the mouse genome like this:
Then I modified arguments in the dynaseq script to my mouse genomeDir path like this
Then I ran the test like this
Sadly this is the point where I get an error message. I looked at the log file (attached 1) and it seems to be a problem that it cannot find the mt_gene_list and gtf files. However, when I go to my genomeDIR I do think that I see these files (attached 2) Do you know how I can fix this problem? I have limited bioinformatics experience, so it is difficult for me to logically describe my problem to you. I hope you understand my question. |
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