User: camerond

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camerond150
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150
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Cardiff
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1 month ago
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2 years, 10 months ago
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c*******@cardiff.ac.uk

Posts by camerond

<prev • 40 results • page 2 of 4 • next >
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Comment: C: Extracting high quality reads from partially failed 10X single cell RNA-, ATAC-s
... Many Thanks @ATpoint. I will try this on Monday. The problem is actually with the R2 reads. The R1 reads are consistently 28bp long. I tried running the files through cell ranger to see what would happen but, in their current state, the software does not recognise the 10X chemistry used in the exper ...
written 10 months ago by camerond150
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Comment: C: Extracting high quality reads from partially failed 10X single cell RNA-, ATAC-s
... We have contacted them, but unfortunately our service contract with the Hiseq 4000, has just ended (we are moving over to the Novaseq for future runs), so I'm not sure we'll get, or whether it's worth getting, anything back from them. We were running this experiment as a test on the samples to see i ...
written 10 months ago by camerond150
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Extracting high quality reads from partially failed 10X single cell RNA-, ATAC-seq sequencing run
... I seek advice as to the best strategy to salvage high quality reads from a 10X single cell RNA-, and ATAC-seq experiment that partially failed on the Hiseq-4000. The issue is mainly with the scRNA-seq data. On the flow cell we ran 5 lanes for RNA and 3 lanes for ATAC. The failure occurred as each ...
10x single cell rna-seq sequencing written 10 months ago by camerond150
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Comment: C: Snakemake: Force execution of rules in a specific order - ignoring wildcards
... @EricLim - Many Thanks. ...
written 11 months 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 11 months ago by camerond150 • updated 11 months ago by Eric Lim1.7k
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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 14 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 14 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 14 months ago by camerond150 • updated 9 months ago by jrmerritt60
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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 18 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 19 months ago by camerond150

Latest awards to camerond

Popular Question 9 weeks ago, created a question with more than 1,000 views. For Snakemake logging error
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Obtaining rsIDs using BiomaRt or linux
Popular Question 8 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
Great Question 10 months ago, created a question with more than 5,000 views. For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
Student 16 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 19 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 20 months ago, voted at least 25 times.
Scholar 20 months ago, created an answer that has been accepted. For A: Snakemake logging error
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Snakemake logging error
Popular Question 2.4 years 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 2.4 years 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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