User: camerond

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camerond60
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1 year, 2 months ago
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c*******@cardiff.ac.uk

Posts by camerond

<prev • 17 results • page 1 of 2 • next >
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Answer: A: Snakemake logging error
... It was a typo in the braces! log: "logs/homer/annotation.ATAC24to31_fetal_hMG.consensusPeak.(THRESH}.log" ...
written 1 day ago by camerond60
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Snakemake logging error
... I'm building a Snakefile and getting an error I'm struggling to fix when trying to add the `log` parameter in my homer annotation rule. Here is the Snakefile: threshold="25 33 5 66 75".split() rule all: input: expand("homer_files/annotation_files/ATAC24to31_fetal_hMG_cons ...
log snakemake written 1 day ago by camerond60
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Comment: C: Issue running deeptools on cluster via snakemake
... Thanks. Re: the threads - I was messing about with this as even though I had `threads: 6` written in the rule when I did snakemake -np the code was coming out saying `threads: 1`, which I found confusing. After what you said above I assume that's because I only have 1 thread available in my `home` l ...
written 8 days ago by camerond60
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Comment: C: Issue running deeptools on cluster via snakemake
... Yes and yes. All the packages I use for this are in a specific environment for this script. The environment the script is in when it is sent to the scheduler is taken as the default environment with variables etc. I have about 12 separate rules using similar path/environmental variables, so assumed ...
written 8 days ago by camerond60
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Issue running deeptools on cluster via snakemake
... I have snakemake Snakefile for an ATAC-seq pipeline that I have been using for ages and I'm trying add a Snakerule to create bigwig files from bam files. I'm using the `bamCoverage` program from the `Deeptools` package to do this. The `snakemake -np` output works fine, and the code snakemake spits ...
deeptools snakemake written 8 days ago by camerond60 • updated 8 days ago by russhh4.4k
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Comment: C: Problems when exporting GRanges file as bigwig after hg38 to hg19 lift over usin
... Thanks for the suggestion, but your right that threw an overlapping error. `Error in FUN(extractROWS(unlisted_X, IRanges(X_elt_start[i], X_elt_end[i])), : BigWig ranges cannot overlap` The vignettes for the packages I used suggest that it is possible to lift over using a bigwig file ... ...
written 5 weeks ago by camerond60
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Problems when exporting GRanges file as bigwig after hg38 to hg19 lift over using rtracklayer and annotation hub
... I'm trying to use `rtracklayer` and `AnnotationHub` in `R` to lift over a `.bw` file I have that is aligned to hg38. I need the data to be aligned to hg19. By following this [vingette][1], I think I have successfully done this using the R packages mentioned above with the code below. library(r ...
R lift over bigwig granges rtracklayer written 5 weeks ago by camerond60 • updated 5 weeks ago by benformatics840
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Comment: C: Obtaining rsIDs using BiomaRt or linux
... Hi @dan_adams Thanks for your response. This suggestion ran for a bit (it takes a while) but after 28 SNPs it threw the following error: Error in `[<-.data.frame`(`*tmp*`, , 5, value = 27L) : replacement has 1 row, data has 0 It's obviously choking as the SNP does not correspond to an ...
written 11 months ago by camerond60
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Obtaining rsIDs using BiomaRt or linux
... I have a list of 390 SNPs that I need to retrieve rsIDs for on the hg19 build. My SNP file is in the following bed format (chromosome start stop). chr1 207679307 207679307 chr1 207684192 207684192 chr1 207685786 207685786 chr1 207685965 207685965 chr1 207692049 207692049 ...
R biomart snps rsid bed written 11 months ago by camerond60 • updated 11 months ago by Pierre Lindenbaum120k
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Comment: C: Get rsID for a list of SNPs in an entire GWAS sumstats file
... Hi finswimmer, Finally got it working and accepted your answer. Thanks for your help. The final issue I was having was with the zipped dbSNP file. When trying to index with tabix it was throwing an error. Zipping had to be done with bgzip, I'd used something else to zip the file initially. The fin ...
written 13 months ago by camerond60

Latest awards to camerond

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
Popular Question 9 months 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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