User: JJ

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JJ320
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Posts by JJ

<prev • 118 results • page 1 of 12 • next >
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Comment: C: Compute Phylogenetic Trees Using Snps Data (VCF files)
... Hi, Sorry for not being clear... I read that it it is important to use a pruned set of SNPs which are in approximate linkage equilibrium with each other to avoid the strong influence of SNP clusters in relatedness analysis (see [here][1]) so I wondered how I can do this in TASSEL. So, is there a wa ...
written 24 days ago by JJ320
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Comment: C: Compute Phylogenetic Trees Using Snps Data (VCF files)
... Hi, I have imported and sorted it already - that's all done. I also made a Cladogram but I could not find anything on how to use a pruned set of SNPs for the computation of the Cladogram - so how can I use the LD for the cladogram? Thanks :) ...
written 27 days ago by JJ320
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Comment: C: Compute Phylogenetic Trees Using Snps Data (VCF files)
... Hi again :) so I've imported my VCFs and ran the Cladogram function. Now I would like to refine it: first with filtering and then with LD There is some information about filtering in the youtube video - something I still have to figure out. Do you have some tips? I have cell line data. Most impor ...
written 27 days ago by JJ320
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Comment: C: Compute Phylogenetic Trees Using Snps Data (VCF files)
... Could you add a link to the tool? Thanks!! ...
written 28 days ago by JJ320
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Compute Phylogenetic Trees Using Snps Data (VCF files)
... Hi all, I was wondering wether there are any new tools to construct phylogenetic trees using SNPs, in particular based on VCF files. I came across three tools/packages [SNPYHLO][1], [snpTree][2] and [SNPRelate][3]. I cannot get SNPYHLO to work - keeps throwing errors (maybe because I work with a ...
snp written 29 days ago by JJ320 • updated 28 days ago by princy14960
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Comment: C: How can I compute if the co-occurrence of two TFBSs within a certain width in al
... Thank you for the links to those tools! They provide a different way of approaching the problem. However, if I have evaluated only the promoter regions for TFBSs wouldn't they automatically produce a positive result since all hits are at least as close as the length of the promoter region I have ev ...
written 9 weeks ago by JJ320
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Comment: C: How can I compute if the co-occurrence of two TFBSs within a certain width in al
... Thanks for your input. So how do I go about the multiple sets of random combinations of TFs? I have the set I am interested in and n number of random combinations of TFs - for each combination I have a set and subset. Do I average the values for set and subset beforehand and then do one Fisher Exac ...
written 9 weeks ago by JJ320
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How can I compute if the co-occurrence of two TFBSs within a certain width in all promoters is larger than by chance?
... Hi, I have computed the number of co-occurrences of two TFBSs in all promoters in the human genome. [Previously][1], we have discussed how to calculate if the co-occurring of two TFBSs is higher than one would expect by chance, which can be done with a hypergeometric distribution using the princi ...
genome sequence written 9 weeks ago by JJ320 • updated 9 weeks ago by dariober9.2k
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Comment: C: Calculate if the co-occurring of two TFBSs is higher than one would expect by ch
... Yes, of course these are two completely different questions - both interesting A third question I am interested in would be if co-occurrence within a certain width is higher than chance. So let's say within 100 bp of one another in all promoters (or even genome). So these are then a subset of the c ...
written 10 weeks ago by JJ320
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Comment: C: Calculate if the co-occurring of two TFBSs is higher than one would expect by ch
... Thank you very much for your input!!! ...
written 10 weeks ago by JJ320

Latest awards to JJ

Popular Question 22 days ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Centurion 10 weeks ago, created 100 posts.
Student 11 weeks ago, asked a question with at least 3 up-votes. For Scanning for TFBSs of known motifs in all human promoters
Scholar 12 weeks ago, created an answer that has been accepted. For A: Gene Expression data and variants from the same fastqc raw file
Supporter 8 months ago, voted at least 25 times.
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Help in writing NGS pipeline (or: the road from fasta to vcf)

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