User: camerond

gravatar for camerond
camerond150
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150
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Cardiff
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3 hours ago
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2 years, 12 months ago
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c*******@cardiff.ac.uk

Posts by camerond

<prev • 41 results • page 1 of 5 • next >
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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 camerond150
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Comment: C: Seurat - label cells in cluster plot by transcripts per cell
... Yes - that's the one. Many Thanks. Wrong function! ...
written 4 months ago by camerond150
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Seurat - label cells in cluster plot by transcripts per cell
... 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 ...
single-cell cluster labelling seurat rna-seq written 4 months ago by camerond150 • updated 4 months ago by rpolicastro4.0k
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Comment: C: Snakemake - moving, re-naming, unzipping and merging files for downstream analys
... 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 camerond150
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Comment: C: Snakemake - moving, re-naming, unzipping and merging files for downstream analys
... Ah ... I didn't know that. Thanks for the heads up! ...
written 8 months ago by camerond150
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Comment: C: Snakemake - moving, re-naming, unzipping and merging files for downstream analys
... 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 camerond150
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Comment: C: Snakemake - moving, re-naming, unzipping and merging files for downstream analys
... 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 camerond150
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Comment: C: Snakemake - moving, re-naming, unzipping and merging files for downstream analys
... 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 camerond150
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Snakemake - moving, re-naming, unzipping and merging files for downstream analysis
... 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 ...
merging fastq snakemake python written 8 months ago by camerond150
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Comment: C: Extracting high quality reads from partially failed 10X single cell RNA-, ATAC-s
... No probs. Many Thanks. ...
written 12 months ago by camerond150

Latest awards to camerond

Popular Question 3 months ago, created a question with more than 1,000 views. For Snakemake logging error
Popular Question 4 months ago, created a question with more than 1,000 views. For Obtaining rsIDs using BiomaRt or linux
Popular Question 9 months ago, created a question with more than 1,000 views. For Get rsID for a list of SNPs in an entire GWAS sumstats file
Great Question 11 months ago, created a question with more than 5,000 views. For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
Student 18 months ago, asked a question with at least 3 up-votes. For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
Popular Question 21 months ago, created a question with more than 1,000 views. For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
Supporter 21 months ago, voted at least 25 times.
Scholar 21 months ago, created an answer that has been accepted. For A: Snakemake logging error
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Snakemake logging error
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Get rsID for a list of SNPs in an entire GWAS sumstats file
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations

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