User: camerond
camerond • 90
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Posts by camerond
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... 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 + +++++++++++++++++++++++++
...
written 10 weeks ago by
camerond • 90
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... @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
camerond • 90
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... 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 ...
written 3 months ago by
camerond • 90
• updated
3 months ago by
Jeremy Leipzig ♦ 18k
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... Many Thanks @shawn.w.foley
Your explanation will help me on future munging attempts. ...
written 3 months ago by
camerond • 90
6
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2
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126
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6 follow
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... 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 ...
written 3 months ago by
camerond • 90
• updated
3 months ago by
shawn.w.foley • 1.0k
3
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1
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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
camerond • 90
4
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1
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255
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1
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... 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 ...
written 3 months ago by
camerond • 90
0
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1
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... 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
camerond • 90
0
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1
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287
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... 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
camerond • 90
5
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1
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287
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1
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... 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 ...
Latest awards to camerond
Popular Question
3 months ago,
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For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
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12 months ago,
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For Get rsID for a list of SNPs in an entire GWAS sumstats file
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For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
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