User: camerond

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camerond90
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Posts by camerond

<prev • 22 results • page 1 of 3 • next >
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One tool for get genome co-ordinates from rsIDs GWAS sumstats files, then liftOver from hg18 to hg19?
... I have 4 fairly old GWAS files from 2010 and I need to use one of them for a negative control in my analyses. The format of the files are as follows: MarkerName Allele1 Allele2 Weight GC.Zscore GC.Pvalue Overall Direction rs629301 t g 100184.00 24.350 5.77e-131 + +++++++++++++++++++++++++ ...
liftover gwas sumstats snp linux written 10 weeks ago by camerond90
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Comment: C: Appropriate use of wildcards for single instances in Snakemake
... @Jeremy Leipzig Thanks for the suggestion. Unfortunately this will not work for me as the program produces single output file for all chromosomes. Your suggestion creates an individual output file for each chromosome in a separate folder. I'm wondering of if I can work around this somehow by sending ...
written 3 months ago by camerond90
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Appropriate use of wildcards for single instances in Snakemake
... I'm using `snakemake` to automate Garfield GWAS SNP enrichment analyses over multiple annotations. My issue is with the variable `{CHR}` in the snakefile below: import os # read config info into this namespace configfile: "config.yaml" rule all: input: expand("garfiel ...
wildcards snakemake garfield written 3 months ago by camerond90 • updated 3 months ago by Jeremy Leipzig18k
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Comment: C: Extract and retain only chromosome info in GWAS sumstats file
... Many Thanks @shawn.w.foley Your explanation will help me on future munging attempts. ...
written 3 months ago by camerond90
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Extract and retain only chromosome info in GWAS sumstats file
... I have a GWAS sumstats file called `sumstats.txt` in the following format: SNP Freq.A1 CHR BP A1 A2 OR SE P 10:100968448:T:AA 0.3519 10 100968448 t aa 1.0024 0.01 0.812 10:101574552:A:ATG 0.4493 10 101574552 ...
bash sed gwas sumstats munging awk written 3 months ago by camerond90 • updated 3 months ago by shawn.w.foley1.0k
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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 3 months ago by camerond90
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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 3 months ago by camerond90
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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 4 months ago by camerond90
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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 4 months ago by camerond90
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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 4 months ago by camerond90 • updated 4 months ago by russhh4.7k

Latest awards to camerond

Popular Question 3 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 3 months ago, voted at least 25 times.
Scholar 3 months ago, created an answer that has been accepted. For A: Snakemake logging error
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Snakemake logging error
Popular Question 12 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 12 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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