User: pfs

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pfs250
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Posts by pfs

<prev • 46 results • page 1 of 5 • next >
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Comment: C: De-replicating sequence file after barcodes/primers removed.
... What does the 'orig_bc=*' identifier stand for? ...
written 6 months ago by pfs250
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Answer: A: Multiple testing correction in linear mixed models (MLM) for GWAS
... Bonferroni correction ...
written 6 months ago by pfs250
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Answer: A: Where can I find the info about the start/end position of sets of SNP's that are
... For diversity based haploblock see Alfred's database. Ethnic breakdown of haplotypes will be available for at least the haploblocks discussed in this paper (https://www.sciencedirect.com/science/article/pii/S1872497317300613?via%3Dihub#upi0010). Another source would be to use STRs. See link for ...
written 12 months ago by pfs250
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Comment: C: how to combain microarray sets from the same platform but raw data were normaliz
... Yes, I would recommend downloading the cel files, loading these files in R, then using the R program LIMMA to normalize each dataset using the same normalization method and then perform your analysis. There may be better programs than LIMMA but if I recall correctly you should be able to do the dat ...
written 13 months ago by pfs250
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Answer: A: how to combain microarray sets from the same platform but raw data were normaliz
... It looks like you can download the raw data for all three microarray datasets. I would take the raw data and implement the same normalization methods on each and then perform the analysis? ...
written 13 months ago by pfs250
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Answer: A: Regenotype vcf using some samples as reference
... If you care about comparing the case vs controls then you still have two differences. The C's are homozygous Major while the T's are heterozygous for var 2, and the opposite for var 3. The major and minor reference allele do not always result in in optimal/not optimal gene expression. You should ...
written 13 months ago by pfs250
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Answer: A: finding function of genes from their coordinates
... I would start here https://www.ncbi.nlm.nih.gov/protein/. If you have a manhattan plot of SNPs then you may want to annotate the SNPs using an annotation program such ANNOVAR to determine the what your SNP may actually be effecting. ...
written 13 months ago by pfs250
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Answer: A: Merging data coloum wise in R
... Look into the merge command. ...
written 13 months ago by pfs250
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Comment: C: Samtools mpileup ends abruptly without completing full analysis
... Default mpileup will only output variants. Are you anticipating variants in all your bam files? ...
written 14 months ago by pfs250
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Comment: C: Given QTLs and genome annotation, quickly list genes closest to QTLs
... I do not have first hand experience doing this but the 'Experimental Design' section in 'Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR' should get you started. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4718734/ ...
written 14 months ago by pfs250

Latest awards to pfs

Appreciated 7 months ago, created a post with more than 5 votes. For A: (Sanity check) Too many SNPs?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to find the unique list of mismatches of reads with the reference genome
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to find the unique list of mismatches of reads with the reference genome
Scholar 15 months ago, created an answer that has been accepted. For A: How to find the unique list of mismatches of reads with the reference genome
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How to find the unique list of mismatches of reads with the reference genome
Scholar 16 months ago, created an answer that has been accepted. For A: How to find the unique list of mismatches of reads with the reference genome
Scholar 16 months ago, created an answer that has been accepted. For A: How to find the unique list of mismatches of reads with the reference genome
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: How to find the unique list of mismatches of reads with the reference genome

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