User: pfs

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pfs250
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Posts by pfs

<prev • 44 results • page 1 of 5 • next >
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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 5 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 6 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 6 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 6 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 6 months ago by pfs250
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Answer: A: Merging data coloum wise in R
... Look into the merge command. ...
written 6 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 6 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 7 months ago by pfs250
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Comment: C: how to annotate chromosome position with the gene list file
... This looks like a bedtools intersect problem. What command did you use? ...
written 7 months ago by pfs250
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Answer: A: Suggestions regarding bioinformatics journal
... I would post the article on a non-peer reviewed site first so you get your work out there and claim the space. See https://www.biorxiv.org/. In your situation I would just submit the article to another journal. ...
written 7 months ago by pfs250

Latest awards to pfs

Appreciated 13 days ago, created a post with more than 5 votes. For A: (Sanity check) Too many SNPs?
Teacher 7 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 7 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 8 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 8 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 9 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 9 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 9 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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