User: lamia_203

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lamia_20350
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Posts by lamia_203

<prev • 22 results • page 1 of 3 • next >
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Parallelise Watermelon Dasen normalisation
... Hi, I'm running quality control on 2 thousand samples and normalisation using the dasen function (from watermelon) - however it takes hours for this to run. I have attached the code below and want to parallelise the function to normalize.quantiles each type of probe at the same time on different c ...
watermelon parallelise epic array normalisation R written 11 days ago by lamia_20350
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Comment: C: Multiple commands in a for loop
... I'll take note thank you. It worked with the semi-colon but still produces outputs. I wanted to carry the amended file each command carries out onto the next command and avoid using the origin file each time as well as producing those files in the shell but it looks like the latter occurred. ...
written 5 weeks ago by lamia_20350
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Comment: C: Multiple commands in a for loop
... Thank you that has worked, but awk still appears with 'plink.awk' so I still have to edit commans once pasted on the shell. All my file names start with plink. but I'm not sure why the attach to the awk command. ...
written 5 weeks ago by lamia_20350
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Multiple commands in a for loop
... Hi, I am trying to make multiple commands within a for loop but it is not working as awk appears as plink.awk once pasted on the shell. I've written the command below. I have attempted to pipe is as I do not need intermediate files. Any help would be much appreciated, thank you! for f *.linear; ...
genome loops sequence unix bash written 5 weeks ago by lamia_20350
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Generating Forest Plots for Meta-Analysis from METAL outputs
... Hi, sorry for asking a simple maths question but I have been unable to plot any forest plots as my data is not comparable. I have ran a GWAS using plink and the outputs include; effect size, t-statistics and SE. However, the meta-analysis I ran outputs Z-scores and direction. I'm not sure how to mak ...
R meta-analysis forest plots statistics written 5 weeks ago by lamia_20350
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METAL Output Effect size calculation
... Hi. I am running a GWAS meta-analysis using METAL. The outputs are Weight, Zscore, P-value and Direction. I want to calculate the effect size and standard deviation. The z-score indicates some form of direction of variance from mean but how can calculate the effect size of a snp? Any help is mu ...
R metaanalysis z score metal effect size written 6 weeks ago by lamia_20350
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How to combine count matrix with mouse gene information from Ensemble using Biomart in R
... Hi, I am trying to add a row of gene id next to my rows of gene symbols. normlaised_mouse3 is my count matrix for rna-seq analysis. I've used to code: library('biomaRt') normalised_mouse_biomart <- read.delim("normalised_mouse3.txt") mart <- useDataset("mmusculus_gene_ensembl", u ...
ensembl biomart rna-seq R written 11 months ago by lamia_20350 • updated 11 months ago by zx87549.0k
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Comment: C: Aligning using hg18
... The genome was used before and aligned fine and gave reads at expected genes for another study I carried out (beta cells), however I am also unsure as to why it didn't map the reads I provided (they are human as well). The parameters were kept the same as before as well: for i in *.fq.gz; do ST ...
written 12 months ago by lamia_20350
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Comment: C: Aligning using hg18
... Thank you. I downloaded it from [UCSC][1] I believe, I couldn't find the gtf files clearly on there. This is my first time downloading genomes hence why I am unclear. [1]: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ ...
written 12 months ago by lamia_20350 • updated 12 months ago by RamRS25k
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Comment: C: Aligning using hg18
... Many thanks! Yes, I tried aligning it to recent genome GRCh38 but the counts all appeared as 0 for genes and were all unmapped after QC. So I am trying to align the samples to the genome that the study have used. I am not sure why there were unmapped reads for GRCh38 as I had used it to previously a ...
written 12 months ago by lamia_20350

Latest awards to lamia_203

Popular Question 5 weeks ago, created a question with more than 1,000 views. For How to speed up trimming using trim galorer
Popular Question 9 months ago, created a question with more than 1,000 views. For Creating Count Matrix
Popular Question 9 months ago, created a question with more than 1,000 views. For Alignment loop using STAR

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