User: Mamta

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Mamta440
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440
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United States
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2 months, 3 weeks ago
Joined:
7 years, 11 months ago
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Posts by Mamta

<prev • 139 results • page 1 of 14 • next >
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Comment: C: Single cell rnaseq analysis pipeline available
... HI Shicheng, I haven't yet- but thats a great suggestion. Will look into it. Mamta ...
written 3 months ago by Mamta440
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Tool: Single cell rnaseq analysis pipeline available
... Hi all, I have created an automated script that takes your raw files from cell ranger and creates an integrated clustered Seurat object that can be used for visualization and downstream analysis. Also- there is an visualization app available that takes the object created from the above script and pl ...
chromium10x scrna seurat scrnaseq tool written 3 months ago by Mamta440
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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 2.1 years ago by Mamta440 • updated 22 months ago by pfs270
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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 2.6 years ago by Mamta440
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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 3.2 years ago by Mamta440 • updated 6 months ago by Hasanga0
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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 3.2 years ago by Mamta440 • updated 3.0 years 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 3.2 years ago by Mamta440
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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 3.2 years ago by Mamta440 • updated 3.2 years ago by natasha.sernova3.6k
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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 3.2 years ago by Mamta440 • updated 3.2 years ago by ivivek_ngs4.8k
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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 3.2 years ago by Mamta440

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