User: fr

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fr130
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Posts by fr

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Comment: C: RNAseq: should I trim both 3' and 5'?
... Thanks, found this thanks to your comment: https://emea.support.illumina.com/bulletins/2016/04/adapter-trimming-why-are-adapter-sequences-trimmed-from-only-the--ends-of-reads.html ...
written 7 weeks ago by fr130
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RNAseq: should I trim both 3' and 5'?
... I'm running an RNAseq analysis that was sequenced in Illumina HiSeq 2500. From [the reference docs](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences-1000000002694-12.pdf) I can see that adapters a ...
rna-seq written 7 weeks ago by fr130 • updated 7 weeks ago by swbarnes27.9k
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Comment: C: Computing significance of overlap between two gene lists in Python
... @Mensur, thanks for your comment. Perhaps I'm missing something, but I do not want to compare 2 distributions, I want to assess the likelihood of getting the overlap between subgroups out of chance. ...
written 11 weeks ago by fr130
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Computing significance of overlap between two gene lists in Python
... I have two gene lists, derived from two independent datasets. I want to compute the significance of overlap between two subgroups. This is the case of 2 lists of differentially expressed genes in each dataset. I want to know whether the overlap between both groups would be given by chance. For inst ...
python hypergeometric fishers written 11 weeks ago by fr130 • updated 5 weeks ago by Biostar ♦♦ 20
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RNAseq: differences when shifting from 100bp to 150bp?
... Our colleagues have previously sequenced data using NovaSeq 100bp PE reads. However, now they changed to 150bp PE reads and I'm wondering whether results will be comparable with those of the 100bp PE if: - they proceed as usual with the 150bp PE reads - they trim the results from 150bp to 100bp ...
rna-seq written 3 months ago by fr130
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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 5 months 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 6 months 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 6 months 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 7 months 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 7 months ago by fr130

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