User: panacotaforcota

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Posts by panacotaforcota

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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 12 weeks 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 12 weeks ago by panacotaforcota0 • updated 12 weeks ago by ATpoint36k
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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 3 months ago by panacotaforcota0 • updated 3 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 9 months ago by panacotaforcota0 • updated 9 months ago by ATpoint36k
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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 10 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 10 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 10 months ago by panacotaforcota0
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H3K4me3 in promoter regions, which are free of nucleosomes
... Hello! I'm trying to deal with histone mark and their localization on the genome. I read that marks H3K4me3 are localized in the promoter regions. But I know that promoters are free of nucleosomes. How is this possible? Do I understand correctly that the presence of histone marks from an experiment ...
h3k4me3 promoter chip-seq nucleosome written 10 months ago by panacotaforcota0 • updated 10 months ago by ATpoint36k

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