User: camerond

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camerond150
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Posts by camerond

<prev • 27 results • page 1 of 3 • next >
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Comment: C: Snakemake: Force execution of rules in a specific order - ignoring wildcards
... @EricLim - Many Thanks. ...
written 5 days ago by camerond150
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Snakemake: Force execution of rules in a specific order - ignoring wildcards
... 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 ...
python snakemake rule execution written 8 days ago by camerond150 • updated 8 days ago by Eric Lim1.6k
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Answer: A: Using bedtools intersect on multiple bed files to retain peaks in 2 out of 3 fil
... 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 camerond150
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Comment: C: Using bedtools intersect on multiple bed files to retain peaks in 2 out of 3 fil
... @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 camerond150
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Using bedtools intersect on multiple bed files to retain peaks in 2 out of 3 files
... 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 ...
bedtools intersect bed file written 3 months ago by camerond150
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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 7 months ago by camerond150
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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 8 months ago by camerond150
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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 8 months ago by camerond150 • updated 8 months ago by Jeremy Leipzig19k
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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 9 months ago by camerond150
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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 9 months ago by camerond150 • updated 9 months ago by shawn.w.foley1.2k

Latest awards to camerond

Student 5 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 8 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 9 months ago, voted at least 25 times.
Scholar 9 months ago, created an answer that has been accepted. For A: Snakemake logging error
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Snakemake logging error
Popular Question 18 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 18 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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