User: lamia_203

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lamia_20390
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Posts by lamia_203

<prev • 22 results • page 1 of 3 • next >
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Masking Y chromosomes
... Hi, I am working on masking chromosome on the Y chromosome. I can see that I need a mask.bed file for input but do not understand how to generate the mask.bed file itself. Is the mask.bed file the coordinates of the chromosome? This is the code I would be using: xyalign --PREPARE_REF ...
genome whole generation sequencing wgs bash written 9 weeks ago by lamia_20390 • updated 9 weeks ago by Jorge Amigo12k
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Comment: C: Meta-Analysis effect size is not in the same direction as GWAS effect sizes.
... Thank your for the response and confirming the estimate values in R. I've looked at the meta analysis alleles and they are flipped. Not sure how that has occurred but it makes sense why your estimate value is the same as mine but the sign is the opposite. Many thanks for your help! ...
written 10 months ago by lamia_20390
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Comment: C: Meta-Analysis effect size is not in the same direction as GWAS effect sizes.
... Yes, I've pulled the most significant SNP from the meta-analysis then used that SNP to select from the other studies. I've managed to sort it out - the allele direction was flipped hence the correct absolute effect size but incorrect direction. I'm not sure how that has happened to some files and no ...
written 10 months ago by lamia_20390
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Meta-Analysis effect size is not in the same direction as GWAS effect sizes.
... Hi, I am conducting a meta-analysis and the output doesn't make sense. I ran gwas on several different treatments and some treatments work well, other do not. The effect size for the 3 gwas results are 0.016,0.012 and 0.011 with respective SE of 0.005,0.005,0.004. However the effect size for the m ...
R metal meta-analysis gwas written 10 months ago by lamia_20390 • updated 10 months ago by Lemire600
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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 12 months ago by lamia_20390
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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 12 months ago by lamia_20390
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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 12 months ago by lamia_20390
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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 22 months ago by lamia_20390 • updated 22 months ago by zx87549.9k
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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 23 months ago by lamia_20390
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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 23 months ago by lamia_20390 • updated 23 months ago by _r_am32k

Latest awards to lamia_203

Popular Question 17 days ago, created a question with more than 1,000 views. For Creating Count Matrix
Student 6 weeks ago, asked a question with at least 3 up-votes. For How to speed up trimming using trim galorer
Popular Question 12 months ago, created a question with more than 1,000 views. For How to speed up trimming using trim galorer
Popular Question 20 months ago, created a question with more than 1,000 views. For Creating Count Matrix
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