User: camerond
camerond • 150
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Posts by camerond
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Comment:
C: cellranger count help
... @Max.Ka. Many thanks for posting this. I had the same issue trying to run cellranger-atac count and was completely stumped. In a folder containing >200 `fastq.gz` files there was a rogue `.txt` file in there that prevented the the program running. My error message was this:
`Invalid path/pref ...
written 15 days ago by
camerond • 150
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... Yes - that's the one. Many Thanks. Wrong function! ...
written 4 months ago by
camerond • 150
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... I'm trying to create a cluster plot in Seurat where instead of the cluster colours being determined by cluster IDs, they are determined by the the transcripts per cell (`nCount_RNA`).
I have tried to use the `DimPlot()` function for this:
DimPlot(rna, reduction = "umap", label = TRUE, group.by ...
written 4 months ago by
camerond • 150
• updated
4 months ago by
rpolicastro ♦ 4.0k
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... I understand that. The issue is that the `/path/to/file/` and `filenames` of the original 120 files have no consistency. This was the main reason for using pandas in the first rule, in order to standardise, or to use your term, normalise the sample/filenames so that I could start using the typical ` ...
written 8 months ago by
camerond • 150
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... Ah ... I didn't know that. Thanks for the heads up! ...
written 8 months ago by
camerond • 150
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... No probs. Fair points. Most of the snakemake walkthrough/tutorials describe the functionality of `{wildcards}` in relation to a single `{wildcard}` that remains constant and flows through the most, if not all of the rules i.e. `{sample}`. I've yet to find one that describes the best way do deal with ...
written 8 months ago by
camerond • 150
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... Response to first post: Probably, yes. However, I was hoping to standardise the `{wildcards}` across the rules. Your suggestion would add more `{wildcards}`, but that may be the cleanest way to do it. What do you mean pandas may be overkill? What would you suggest as an alternative? ...
written 8 months ago by
camerond • 150
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... Thanks for your suggestions. Re: if statement - Although I think both work, your way is less verbose so I have changed it in the IP.
...
written 8 months ago by
camerond • 150
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... In my current project, I have ~560 RNA-seq fastq files (120 samples) that were sequenced in various locations. As such, the naming structure of the files are different, some files are zipped and some are unzipped, the files are dotted around our databank in various locations and the sample ID for ea ...
written 8 months ago by
camerond • 150
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... No probs. Many Thanks. ...
written 12 months ago by
camerond • 150
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For Snakemake logging error
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