User: QVINTVS_FABIVS_MAXIMVS

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Posts by QVINTVS_FABIVS_MAXIMVS

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Comment: C: R corrplot: combining pvalues and correlations (Brainstorm Figure)
... yeah per the legend I imagine I could fabricate my own set of Pvalues to make it. I think the easiest thing to do perhaps is to hack the corrplot function to switch the variables for coloring ...
written 6 weeks ago by QVINTVS_FABIVS_MAXIMVS2.4k
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Comment: C: R corrplot: combining pvalues and correlations (Brainstorm Figure)
... Yes it's confusing me quite a bit too. Thanks for the confidence in my sanity. They are not correlating pvalues but showing the pvalue of the strength of the pairwise correlation, I don't see how they could have made this plot because corrplot it seems you cannot separate the size of the square from ...
written 6 weeks ago by QVINTVS_FABIVS_MAXIMVS2.4k
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R corrplot: combining pvalues and correlations (Brainstorm Figure)
... Hi All I am a little lost at how to replicate this figure. I imagine the authors used corrplot in R to make it ![plot to replicate][1] [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097237/bin/nihms-979389-f0002.jpg With corrplot I am able to make a figure that has the size of the squares ...
R corrplot written 6 weeks ago by QVINTVS_FABIVS_MAXIMVS2.4k
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Comment: C: Determine Reading Frame from Exon Genomic Positions (rMATS)
... Do you have an example because I tried using blastx on my skipped exon sequence and it didn't return anything. The exon is annotated in a GTF in RefSeq which is odd. ...
written 3 months ago by QVINTVS_FABIVS_MAXIMVS2.4k
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Determine Reading Frame from Exon Genomic Positions (rMATS)
... I realize that given an exon start and stop position, the reading frame CANNOT be inferred by starting at the start position making codons. So my question is how to computationally determine the reading frame of an exon given the START and END positions? Specifically I am using the output from rM ...
rmats genome rna-seq written 3 months ago by QVINTVS_FABIVS_MAXIMVS2.4k • updated 3 months ago by swbarnes29.4k
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Comment: C: Ensembl FTP Mirror in USA? Slow Downloads
... Thanks I submitted a ticket. Hopefully they will clear it up. ...
written 4 months ago by QVINTVS_FABIVS_MAXIMVS2.4k
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Comment: C: Ensembl FTP Mirror in USA? Slow Downloads
... ``` $ curl -O ftp://ftp.ensembl.org/pub/release-101/variation/indexed_vep_cache/homo_sapiens_merged_vep_101_GRCh38.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 16.4G 0 13.8M ...
written 4 months ago by QVINTVS_FABIVS_MAXIMVS2.4k
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Ensembl FTP Mirror in USA? Slow Downloads
... Hello I work on a fairly good cluster at an R1 university in the USA. I am downloading the VEP 101 indexed cache files and it's slow as Christmas. I mean AOL speeds slow. If I download a similar size file from AWS or NCBI it's extremely fast. Is there a mirror for the USA containing the VEP cache ...
ensembl vep written 4 months ago by QVINTVS_FABIVS_MAXIMVS2.4k
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Comment: C: Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotatio
... Hey this is a great example. I mentor undergrads in my lab and they could use this video from time to time! Thanks for sharing ...
written 5 months ago by QVINTVS_FABIVS_MAXIMVS2.4k
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MarkDups takes much longer than expected???
... In the past, my 40x WGS BAMs take about 2-6 hours to run sambamba markdups with 12-24 threads. I have received a batch of BAMs that are taking over 7 days to run. The file size is the same, and so is the sequencing center. Any ideas what could cause this step to take much longer than expected? ...
markdup sambamba written 10 months ago by QVINTVS_FABIVS_MAXIMVS2.4k • updated 9 months ago by Biostar ♦♦ 20

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