User: panacotaforcota

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Posts by panacotaforcota

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Reverse allele frequency
... But X and Y axis from 0 to 1. In MAF case 0.5 is upper limit. ...
written 6 months ago by panacotaforcota0
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Comment: C: Reverse allele frequency
... By my own script. Briefly, I change allele frequency as (1-freq) in the reference data if alleles were reverse, for example, in GWAS - A:T, in reference - T:A. There is no mistake. ...
written 6 months ago by panacotaforcota0
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Reverse allele frequency
... Hello! I have a problem with reverse allele frequency in my GWAS. I compare the allele frequency of SNP from GWAS with reference allele frequency. My results after synchronization allele: ![X - reference frequency; Y - GWAS frequency][1] So, I want to understand how I can detect such SNPs to remo ...
gwas frequency allele written 6 months ago by panacotaforcota0
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Comment: C: RegioneR library in R
... Yes, and there are no explanation why for different z-score there are the same p-value. ...
written 9 months ago by panacotaforcota0
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RegioneR library in R
... Hello! I try to use regioneR library in R for permutation test. I get result, where z-score is equal to 79 or -90 and p-value is equal to 0.002 for both z-scores. Number of permutations is 500. I don't understand how those z-score and p-value are calculated. Thanks! ...
R permutation test written 9 months ago by panacotaforcota0 • updated 9 months ago by ATpoint44k
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(Closed) H3K4me3 and GC-rich promoters
... Hi friends! I have a question about the relationship of histone mark H3K4me3 and GC-rich promoters. I know that there is a connection between them, but I can not find articles on this topic. I would like to know the articles explaining this connection. Thanks! ...
h3k4me3 histone mark promoter gc-rich written 9 months ago by panacotaforcota0 • updated 9 months ago by waneryixiao7100
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Stringtie and prepDE
... Hello! I try to use Stringtie to generate read coverage tables for prepDE.py. So, I do ./stringtie-2.0.3/stringtie file_sorted.bam -B -e -G merged.gtf > file.gtf Is it correct that this command return gtf file or not? Then I do ./prepDE.py -i file.gtf -g ./gene.counts.csv -t ./transc ...
stringtie written 15 months ago by panacotaforcota0 • updated 15 months ago by ATpoint44k
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Condition of the chromosomes during the Chip-seq experiment for histone marks.
... Hello! In which condition are chromosomes during the Chip-seq experiment for histone marks? Is it interphase or mitotic state? ...
chip-seq written 17 months ago by panacotaforcota0
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Comment: C: H3K4me3 in promoter regions, which are free of nucleosomes
... Thank you for these articles! Exactly what is needed! ...
written 17 months ago by panacotaforcota0
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Comment: C: H3K4me3 in promoter regions, which are free of nucleosomes
... Thank you very much! It becomes clearer. So, is it true that the data from the Chip-seq experiment correspond to the active state? Or is it an inactive state, but with histone marks that are there all the time? ...
written 17 months ago by panacotaforcota0

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