User: Xianjun

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Xianjun230
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a genome reader

Posts by Xianjun

<prev • 27 results • page 1 of 3 • next >
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Comment: C: How to generate random genomic sequences that are GC- and length-matched to my i
... yes, that's also what I have in my mind so far. I am wondering if any "better" background (e.g. part of genomic region). I like the idea of [http://opossum.cisreg.ca/GC_compo/][1] in oPOSSUM, where they use background regions as human open chromatin regions compiled from the ***lowest*** scoring ChI ...
written 3 months ago by Xianjun230
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Comment: C: How to generate random genomic sequences that are GC- and length-matched to my i
... Sure. I thought there might already be some tools available since it's a common task when people are asked to compare to a length- and GC-matched background set, e.g. TFBS enrichment analysis. ...
written 3 months ago by Xianjun230
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Comment: C: How to generate random genomic sequences that are GC- and length-matched to my i
... Thanks for the reply. I looked into the option of [randomreads.sh][1], right it can produce fasta files, but it doesn't match the length distribution and GC content. [1]: https://github.com/BioInfoTools/BBMap/blob/master/sh/randomreads.sh ...
written 3 months ago by Xianjun230
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How to generate random genomic sequences that are GC- and length-matched to my input sequences?
... Hi, I want to generate a list of random genomic sequences that match GC-content and length to my input DNA sequences. Note that my input sequences are not of the same length. My expected output will be the same number of random sequences that match length and GC-content to the ***individual*** inp ...
gc sequence background random written 3 months ago by Xianjun230 • updated 3 months ago by dariober9.2k
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Answer: A: heatmap.2 reorder branches
... I had the same problem of using the order function with proper weight, and I just figured out the trick. Taking the `mtcars` dataset in e.rempel's example above, we first run the default `hclust` to get the dendrogram. data(mtcars) x <- as.matrix(head(mtcars)) # only using the first 6 ...
written 12 months ago by Xianjun230
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Answer: A: Illumina'S Genome Studio Final Report: Forward Or Top Allele?
... For those who are still not clear with the difference columns in the FinalReport.txt (from GenomeStudio), e.g. Allele1 - Forward, Allele2 - Forward, Allele1 - Top, Allele2 - Top, Allele1 - Plus, Allele2 - Plus, a short answer is: TOP/BOT is for Illumina's own strand designations (which is pretty sma ...
written 20 months ago by Xianjun230
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Comment: C: How to correctly use the color option in R image() function?
... Thanks for your comments, Deepak.  As my reply below, I guess I figured it out: We always get min(x)=col[1], max(x)=col[last]. For your case, then there are 6 colors, again, 1=blue, 3=grey, 2=green (since it's left close). ...
written 3.2 years ago by Xianjun230
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Answer: A: How to correctly use the color option in R image() function?
... OK I figured it out myself:  Unless the breaks is set, the range of Z (or x in above example) is evenly cut into N intervals (where N = the length of color) and values in Z are proportionally assigned to the nearest color. For example, when x=c(3,1,2,1) and col=c("blue","red",'green','yellow'), th ...
written 3.2 years ago by Xianjun230
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How to correctly use the color option in R image() function?
... HI, I got a question about how to assign color value in image() function. I thought the col option works as a vector with the same length of Z, with color of each cell in the matrix Z corresponding to the values in. However, it confused me with different result. To make my question simple, let's s ...
image R written 3.2 years ago by Xianjun230
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Answer: A: Bed File With Introns Only
... Here is an easy example code to convert bed12 --> intron, 5' UTR, 3' UTR, CDS etc.  http://onetipperday.blogspot.com/2012/11/get-intron-utr-cds-from-bed12-format.html If you want to get meta-intron (i.e. merge overlapped introns from one gene into one intron), you can use the code snip below: ...
written 3.2 years ago by Xianjun230

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Popular Question 12 months ago, created a question with more than 1,000 views. For Computational Biologist In Brain Research, Harvard Medical School, Boston, Us
Great Question 16 months ago, created a question with more than 5,000 views. For Any Quick Sort Method For Large Bed File As 20G In Size?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Computational Biologist In Brain Research, Harvard Medical School, Boston, Us
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Computational Biologist In Brain Research, Harvard Medical School, Boston, Us
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: How to correctly use the color option in R image() function?
Scholar 3.2 years ago, created an answer that has been accepted. For A: How to correctly use the color option in R image() function?
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