User: David_emir

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David_emir210
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Posts by David_emir

<prev • 87 results • page 1 of 9 • next >
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Merging data coloum wise in R
... Hello All, I am using R to merge two different CSV file into one new file. both of them has got gene name (1st column) same and the subsequent columns will be my sample ID, I need the output file as follow' 1st_file.csv Gene sample1 sample2 smpleN a 1 4 7 b 2 5 8 c 3 6 9 2nd_file ...
R csv written 11 days ago by David_emir210 • updated 11 days ago by biplab40
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Comment: C: phasing with Eagle
... Thanks a lot For replying, can you please let me know the best possible way to split a file. Please treat my knowledge about this as a beginner .Should i split files for all the chromosome and run phasing on it? Individually? please let me know the best possible way for it. Thanks a lot for your kin ...
written 29 days ago by David_emir210
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Comment: C: Eagle 2 - Phasing
... Thanks Pierre, by any chance can you help me with a solution for this? ...
written 29 days ago by David_emir210
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(Closed) Eagle 2 - Phasing
... Hello All, I am working on a .vcf file with 200 samples and it looks like as follows #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR2098177 SRR2098178 1 10146 . AC A 16738.1 VQSRTrancheINDEL99.00to99.90 . GT:AD:DP:GQ:P ...
eagle2 vcf phasing written 29 days ago by David_emir210 • updated 29 days ago by genomax40k
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phasing with Eagle
... Hi All, I am trying to do phasing with Eagle (Eagle v2.3.5).i Have a .vcf of 122 samples (human diseased samples). I have referred the [Eagle manual][1] but i am not able to understand --chrome function in it. I ran a command as follows: eagle --vcf split_multiallelic.vcf.gz --geneticMapFile ...
imputation without reference written 4 weeks ago by David_emir210
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Comment: C: Custom Reference panel creation for data imputation from .vcf files
... Thanks a Lot Kevin, I am great full to you. thanks a lot .. ...
written 4 weeks ago by David_emir210
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Comment: C: Custom Reference panel creation for data imputation from .vcf files
... Thanks a Lot Kevin, It would be great if you can help me with the script. I would be thankful for this help. ...
written 4 weeks ago by David_emir210
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Comment: C: Custom Reference panel creation for data imputation from .vcf files
... Thanks a lot Kevin, i am so happy to see a solution, at last! I will try doing this. hopefully i will create my own reference panel. I will go through the impute2 tutorials. I have a question- this reference panel will be compatible with Michigan Imputation Server? ...
written 4 weeks ago by David_emir210
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Custom Reference panel creation for data imputation from .vcf files
... Hello All, I need your help in **creating a reference panel (customized)** which can be used for imputation purpose. I have around 100 VCF files and i am interested in creating my own reference panel for analysis, it would be great if you can share the knowledge on how to create this panel or some ...
reference panel imputation written 5 weeks ago by David_emir210 • updated 5 weeks ago by Kevin Blighe11k
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GitHub-GTEx Pipeline- how to execute ?
... Hello Guys, I am interested on getting Correlations between genotype and tissue-specific gene expression levels. I am trying to replicate the same analysis pattern which was described in [This Paper][1]. I have also came across the following pipeline in gitHub [GitHub-GTEx Pipeline][2], but i am n ...
gtex pipeline execution genotype rna-seq written 5 weeks ago by David_emir210

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