User: fr

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fr130
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Posts by fr

<prev • 104 results • page 1 of 11 • next >
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Comment: C: Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
... Hi, I have generated two tracks, one with positive and the other with negative scores. My idea was to overlay them and thus you see on the same track some values being negative and others positive. I have successfully overlaid them, but both end up showing as positive and the scale allowed is only 0 ...
written 4 weeks ago by fr130
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Homer's findPeaks: normalized Tag counts, Peak Score, and RPKMs
... I was reading [this](https://www.biostars.org/p/278730/) and [this](https://www.biostars.org/p/326797/) posts where it is mentioned that > normalized tag count [is] (equal to RPKM reflecting peak density). But I wonder if this is true: from [homer's docs](http://homer.ucsd.edu/homer/ngs/peaks. ...
homer chip-seq atac-seq written 7 weeks ago by fr130
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meaning of "Total subpeaks" in Homer's mergePeaks?
... Homer's [mergePeaks][1] outputs a column with "Total subpeaks" and I'd like to know what does it exactly mean? I initially thought it could be the total number of peaks (i.e. its maximum would be the same as the number of files to input), but this is not the case as this number can be higher. Thank ...
homer chip-seq atac-seq written 10 weeks ago by fr130
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Comment: C: How to view bigwig files in UCSC with windowed coverage?
... Dear Kevin, thanks so much, this solved my problem! I found a way to get the bedgraphs and it worked. I would just like to ask one final question: in general, when you are computing coverage for visualization in a UCSC, or IGV, what window sizes do you usually use? I understand this is very much ca ...
written 12 weeks ago by fr130
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Comment: C: How to view bigwig files in UCSC with windowed coverage?
... Not anymore, what I got were `.bedGraphs` and `TagDirs` :( ...
written 12 weeks ago by fr130
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Comment: C: How to view bigwig files in UCSC with windowed coverage?
... Kevin, this is great, thanks so much. Do you see a straightforward way to do this if I have everything as `.bedGraph` already? ...
written 12 weeks ago by fr130
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Strange output from Homer findPeaks
... I have ran Homer's `findPeaks` but I find the output to be strange. Even disregarding the column order (which seems messed up), it only shows `1` as every tag count? Could anyone tell me if there's something wrong? This is an ATACseq sample # HOMER Peaks # Peak finding parameters: # tag ...
atacseq homer atac-seq written 12 weeks ago by fr130 • updated 8 weeks ago by panxingxin160
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Comment: C: How to view bigwig files in UCSC
... Thanks for your comment. I may be misunderstanding what you want to say, but I have no problems uploading my data to UCSC. The screenshot I gave is from there actually. I have also updated my question's title as the focus is on the "windows" part ...
written 12 weeks ago by fr130
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How to view bigwig files in UCSC with windowed coverage?
... I am trying to view a few ATACseq and Chipseq bigwig files in UCSC. I have identified the peaks for each file, converted them to bigwig, and was able to upload them and see them in UCSC genome browser. However, what I see in `full` mode is a bunch of vertical lines: ![enter image description here][ ...
atacseq chip-seq ucsc written 12 weeks ago by fr130 • updated 12 weeks ago by Kevin Blighe54k
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How to export more than 1000 entries in IPA
... I have performed a miRNA targetscan, but every time I try to export the results I can only export 1000 (out of the 65 thousand rows). How do you export more than 1000 entries? ...
ingenuity pathway analysis ipa written 3 months ago by fr130 • updated 11 weeks ago by Biostar ♦♦ 20

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