User: Mamta

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Mamta400
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6 years, 4 months ago
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Posts by Mamta

<prev • 137 results • page 1 of 14 • next >
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Conditional analysis on dosage file -what program to use?
... HI all, i have recived some files that I fail to understand the header as the dosage info is ok with 3 probabilities for each sample. This was used for the association analysis in plink list skip0=0 skip1=0 format=3 case-control-freqs PLINK v1.90b3.43 64-bit (13 Nov 2016) Options in effect: --a ...
conditional-analysis gwas association plink written 6 months ago by Mamta400 • updated 3 months ago by pfs230
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SNP2HLA merge dosage files with overlaping samples
... HI, I did imputation with Hapmap and I have my dosage files. But the thing is I overlapped samples with different batches for running imputation (for e.g. 1 through 200 –one batch for imputation, then 150-300 next batch of imputation). Iam stuck as to how do I merge these into one file for associat ...
dosage hla snp snp2hla written 12 months ago by Mamta400
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Duplicates in plink files (same position, same ref allele but different A1 allele)
... HI all, I remove duplicate snaps from my files using --list-duplicate vars. However this does not remove the snps with same position , same ref allele but different A1 - one has 0 ). This creates problem when running shapeit, how do I remove these snaps? Thanks, mamta ...
gwas plink snpchip written 19 months ago by Mamta400
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shapeit2 pre-phasing error- empty hap file
... HI all , iam pre-phasing dataset using shapit2, however i get empty hap file , with additional filename.snp.mm and filename.ind.mm. I was reading that this usually happens with missing snps/ind. But I have already removed that before using plink. Log file below: * > " Checking missingness and ...
pre-phasing gwas shapeit2 written 19 months ago by Mamta400 • updated 17 months ago by Biostar ♦♦ 20
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Comment: C: GWAS from case/control + family based WGS data -how to effectively use together
... Thanks. I will look into them. ...
written 19 months ago by Mamta400
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GWAS from case/control + family based WGS data -how to effectively use together
... HI all, We have a GWAS from case/control run on exomechip. We also have 8 families (not necessarily trios) with affected and unaffected members whole genome sequenced. This is a common disease more prevalent in this ethnic group. I am hoping to use this familial study as a filter for the exomechi ...
gwas familial variant filter written 19 months ago by Mamta400 • updated 19 months ago by natasha.sernova2.8k
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Are mapped reads between 2 regions common?
... Hi all, I have 2 precursor mirna with similar sequence. Reads map to both the miRNAs. In my alignment setting I did not do unique mapping only. Is there a way to check how many reads are shared between two regions and what might be unique? Thanks, Mamta ...
rnaseq unique reads written 20 months ago by Mamta400 • updated 19 months ago by vchris_ngs4.3k
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Composite risk score in GWAS using snp weights
... HI All, I have a list of SNP with weights (provided) and I have another dataset genotype with phenotype known. Iam supposed to calculate the "composite risk score" from this new dataset (have plink files) using the SNP weights provided. Whats tools/programs can I use? Is there a tutorial out there? ...
gwas snp snp-weights riskscore written 20 months ago by Mamta400
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genome browser custom track bigwig upload problem with localhost
... Hi All, Since we cannot use dropbox link anymore, i tried setting up a localhost to upload data to UCSC genome browser as custom track. but for some reason http://localhost/data.bw cannot be opened. Any solutions you guys are aware of? or any other way to upload datafile without an ftp site? Thank ...
bigwig customtrack genomebrowser written 21 months ago by Mamta400
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miRNA target enrichment analysis tool?
... HI All, I have a list of miRNA (dysregulated) and mRNA and I would like do an enrichment analysis to see how specificity (compare the number of targets of miRNA in total vs. targets in the dysregulated gene list provided) If the targets are enriched in the complete genelist. Anyone know of any tool ...
mirna enrichment mirna-target written 22 months ago by Mamta400

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