User: brendaumoh6

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Posts by brendaumoh6

<prev • 34 results • page 1 of 4 • next >
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Comment: C: Extracting Snps with pvalue <5x10-8 from gwas result
... Thanks for the input. I used the previous command with another dataset and there was an output. I then sorted my data and discovered that there was no pvalues at that threshold. In conclusion the problem wasnt from the command but rather from the dataset. ...
written 11 weeks ago by brendaumoh60
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Comment: C: Extracting Snps with pvalue <5x10-8 from gwas result
... CHR SNP POS P 1 rs147324274 11063 0.788453971217744 1 rs144804129 30741 0.3335653075464541 1 rs6602381 51427 0.7555139906863562 1 rs189891329 58396 0.9016132067991081 1 rs114824410 69487 0.4442331191209 ...
written 11 weeks ago by brendaumoh60 • updated 11 weeks ago by Asaf8.4k
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Extracting Snps with pvalue <5x10-8 from gwas result
... I am working on Multivariate GWAS analysis and I have my results output from the analysis. I would like to extract Snps which have the pvalue < 5x10-8. However,I used awk '{ if($4 < 5e-8) { print $1 }}' file | head and awk '{ if($4 < 0.00000005) { print $1 }}' file | head ...
snp written 11 weeks ago by brendaumoh60 • updated 11 weeks ago by Pierre Lindenbaum130k
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Estmating Allele Frquency and Snps number
... Hello all,I am working with a Gwas summary statistics data which was downloaded from GWAS catalog. It doesnt have all the columns needed for my analysis. However it lacks effect Allele Frequency and N (The SNP sample sizes) columns. Please how do I derive Freq and N from estimation for my analysis. ...
summary statistics written 4 months ago by brendaumoh60
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Getting rsid from chr:pos
... Hi there, am working with a summary statistics data that has the following columns as snpid : 10:100000012 10:10000010 10:100000122 10:100000177 I want to convert my snpid to rsid. Although I saw some responses regarding this question, I still cant figure out on how to go about it, I used the too i ...
snp written 4 months ago by brendaumoh60
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Comment: C: LD SCORE ESTIMATION
... I separated my chromosomes into chunks and ran the analysis but it is still taking forever to finish so I also calculated PCs for my dataset and ran the analysis using a --cov flag: python ~/cov-ldsc/ldsc.py --bfile split22 --l2 --ld-wind-cm 20 --cov pca_results2.eigenvec --out covldscore_22 I got a ...
written 4 months ago by brendaumoh60
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LD SCORE ESTIMATION
... How can I estimate Ldscore for a particular population from 1000 genome with a minimal time. I tried computing with this code : python ~/ldsc/ldsc.py --bfile afr_phase3 --l2 --ld-wind-cm 1 --out Africa But it takes a lot of time and it is not actually showing if it is running or not. I need either ...
ldscore written 4 months ago by brendaumoh60
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Comment: C: 1000 genome download
... Am using linux OS, with firefox. Though I had the 'dl=1' attached to my file I renamed the file after downloading it on linux. ...
written 4 months ago by brendaumoh60
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Comment: C: 1000 genome download
... Thank you all,it finally worked. I renamed my .pvar from this all_phase3.pvar.zst?dl=1 to all_phase3.pvar.zst. I also decompressed the .pgen file. ...
written 4 months ago by brendaumoh60
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Comment: C: 1000 genome download
... Same error message output but this time no such directory ".pgen" Start time: Wed Apr 29 14:59:09 2020 193440 MiB RAM detected; reserving 96720 MiB for main workspace. Using up to 16 threads (change this with --threads). Error: Failed to open all_phase3.pgen : No such file or direct ...
written 4 months ago by brendaumoh60 • updated 4 months ago by genomax89k

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