User: camerond
camerond • 150
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Posts by camerond
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... @EricLim - Many Thanks. ...
written 5 days ago by
camerond • 150
3
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1
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... I am running an ATAC-seq pipeline that include rules for LD score regression and Partitioned heritability and I need the execution order of these rules to be sequential.
The `ldsr` rule runs fine, but I'm having issue with the `partitioned_heritability` rule as I need it to run after **all** the fi ...
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... As suggested above by @benformatics I used the following in Snakemake:
rule bedtools_intersect_pairwise_method:
input:
general="general_file.bed",
rep1="file1.bed"
rep2="file2.bed"
rep3="file3.bed"
output:
"FINAL_pairwi ...
written 3 months ago by
camerond • 150
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... @benformatics Yes - I was hoping there was something streamlined for this but perhaps it doesn't exist. Many thanks for the suggestion. ...
written 3 months ago by
camerond • 150
2
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2
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... I have 4 standard bed files, a large general file and three smaller files.
I'd like to run `bedtools intersect` to retain the peaks in the general file that overlap with peaks in at least two of the three smaller files keeping only the peak boundary limits of the general file peaks. This is the ge ...
written 3 months ago by
camerond • 150
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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 7 months ago by
camerond • 150
0
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1
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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 8 months ago by
camerond • 150
2
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1
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395
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1
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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 8 months ago by
camerond • 150
• updated
8 months ago by
Jeremy Leipzig ♦ 19k
1
vote
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209
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... Many Thanks @shawn.w.foley
Your explanation will help me on future munging attempts. ...
written 9 months ago by
camerond • 150
6
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2
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209
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6 follow
2
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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 9 months ago by
camerond • 150
• updated
9 months ago by
shawn.w.foley • 1.2k
Latest awards to camerond
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3 months ago,
created a post with more than 5 votes.
For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
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5 months ago,
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For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
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For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
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18 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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