User: seta

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seta1.0k
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Posts by seta

<prev • 647 results • page 1 of 65 • next >
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Comment: C: VEP output and stop gain mutation
... Thank you friend! I checked the variation database (track: All SNPs (150) from Table browser, but I didn't find GERP score. ...
written 4 days ago by seta1.0k
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Comment: C: VEP output and stop gain mutation
... Hi Ben, Thank you very much for your feedback. Regarding the BLOSUM62 amino acid conservation score, although I read about it, I am not sure for correct interpretation, could you please help me out about it? Also, please kindly let me know if there is any association between this score and Condel r ...
written 4 days ago by seta1.0k
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VEP output and stop gain mutation
... Hi all, I annotated some variations (SNP) using VEP, there are two stop gain mutations, one at 2nd amino acid and another at the 110th amino acid position (the protein has about 300 amino acid). While the VEP says their impact is "HIGH", but it didn't return any value for SIFT or polyphen, could yo ...
ensemble vep emily_ensembl stop gain written 5 days ago by seta1.0k • updated 4 days ago by Ben_Ensembl760
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Comment: C: Allele frequency comparison by Fisher's exact test
... Thanks for your help. I have both, the ref and alt allele count for each SNP from both population, however, I'm not sure how to set and feed them to R for multiple fisher's exact tests and get the p-value for each one. Could please someone help me more on this issue? ...
written 12 days ago by seta1.0k
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Comment: C: Allele frequency comparison by Fisher's exact test
... Thank you for the response. Could you please kindly tell me how I should run multiple, here 3000, Fisher's exact test and store the related p-value for each SNP? ...
written 12 days ago by seta1.0k
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Allele frequency comparison by Fisher's exact test
... Dear friends, I would like to compare the allele frequency of a list containing 3000 SNPs related to a given trait between my population and 1000 genome populations (super populations). For my population, the SNPs derived from whole genome sequencing of about 1000 individuals. But, due to missing ...
allele frequency population fisher's exact test written 13 days ago by seta1.0k
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calculating allele frequency difference or Fst value ?
... Hi all, I would like to determine allele frequency difference of a set of SNPs (say 2500 SNPs) between various populations as my first experience in this regard. I think of using the statistical test (Fisher’exact or chi-square test) with the allele count for it. However, I see the estimating Fst v ...
allele frequency population fst written 22 days ago by seta1.0k
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Alt allele count from 1000 genome project
... Hi all, I would like to compare the Alt allele frequency of a list of thousands SNPs derived from my project with the various populations of 1000 genome project. So, I need alt allele count, could you please help me out how to find this infromation based on GRCh38? here, I read [this post][1] abou ...
alt allele count 1000 genome written 27 days ago by seta1.0k • updated 26 days ago by RamRS19k
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Comment: C: Genomic coordinates from GENCODE annotation file
... Thanks Emily, it sounds easier, however, I tested BioMart with 10 gene names (and also with Entrez ID) and it returned many variants with no information about minor allele, minor allele count and frequency for most of them. Also, I could not find these variants came from 1000 genome (and which popul ...
written 4 weeks ago by seta1.0k
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Comment: C: Genomic coordinates from GENCODE annotation file
... Thanks Pedro, yes, I used all sub features of the genes as you mentioned that I corrected with your help. Just two questions, maybe silly one. In your awk command, why you put ".", "." ? and for promoter section, I think using -l 1000 -r 500, please kindly share me your idea about it? ...
written 4 weeks ago by seta1.0k

Latest awards to seta

Voter 9 weeks ago, voted more than 100 times.
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Differentially expressed gene clustering
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Differentially expressed gene clustering
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Differentially expressed gene clustering
Guru 4 months ago, received more than 100 upvotes.
Great Question 4 months ago, created a question with more than 5,000 views. For Remove unwanted characters from FASTA file
Student 4 months ago, asked a question with at least 3 up-votes. For rRNA contamination in poly A-enriched libraries
Popular Question 4 months ago, created a question with more than 1,000 views. For Please help with comparing several gene ontology (GO) list
Popular Question 4 months ago, created a question with more than 1,000 views. For Please help with comparing several gene ontology (GO) list

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