User: Leonardo Collado Torres
Leonardo Collado Torres • 640
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- http://lcolladotor.git...
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Leonardo Collado Torres, Ph. D., Staff Scientist
Lieber Institute for Brain Development
855 N Wolfe St, Suite 300
Baltimore, MD 21205
Website: http://lcolladotor.github.io/
Posts by Leonardo Collado Torres
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... ```R
download_study('SRP009615', type = 'samples')
2019-08-15 15:25:04 downloading file SRR387777.bw to SRP009615/bw
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387777.bw'
Content type 'text/plain; charset=UTF-8' length 94700336 bytes (90.3 MB)
downloaded 90.3 MB
2019-08-15 15:25:15 ...
written 2 days ago by
Leonardo Collado Torres • 640
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... ```R
hms 0.5.0 2019-07-09 [1] CRAN (R 3.6.1)
htmlTable 1.13.1 2019-01-07 [1] CRAN (R 3.6.1)
htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.6.1)
htmlwidgets 1.3 2018-09-30 [1] CRAN (R 3.6.1)
httr 1.4.1 2019- ...
written 2 days ago by
Leonardo Collado Torres • 640
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... Hi hyp15,
You can download the BigWig files for a study using `download_study(project, type = "samples" )`. Note that `"samples"` is quoted, unlike the one you provided in your code above.
So for example this works for downloading all the BigWig sample files for study SRP009615 (took 2 minutes for ...
written 2 days ago by
Leonardo Collado Torres • 640
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... ## Definitions
We have
`scale_counts(current_bp_counts)` = `current_bp_counts` * (`target_AUC` / `current_AUC` ) / `avg_target_read_Length` = `current_bp_counts` * `targetSize` / `current_AUC`
and
`read_counts(current_bp_counts)` =`current_bp_counts` / `avg_observed_read_length` = `current_bp_ ...
written 8 weeks ago by
Leonardo Collado Torres • 640
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... Hi again,
## (1)
No. Say that we have two samples, one with 45 million reads with an average mapped length of 75 base-pairs. The sum of the total coverage (AUC) for sample 1 is 45 mi * 75 = 3,375 x 10^6 For sample 2, we have 40 million reads with an average mapped length of 80 base-pairs, so sampl ...
written 8 weeks ago by
Leonardo Collado Torres • 640
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... Hi,
For normalizing the coverage and visualizing the base-pair level data as in Figure 1 (top row) of https://f1000research.com/articles/6-1558/v1, we scale the data to the same number of reads (of the same length). In this case it matters that the AUC is the same for each sample after scaling, so ...
written 8 weeks ago by
Leonardo Collado Torres • 640
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... Thanks for posting this answer Chris!
Best,
Leo ...
written 4 months ago by
Leonardo Collado Torres • 640
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... Hi Sheldon,
Apologies for the delay in answering. I was busy trying to finish a paper myself.
The answer is a bit complicated. The short version is that some base pairs of the genome are counted more than once in recount2's gene level files. Within a given gene, a base pair is counted only once as ...
written 4 months ago by
Leonardo Collado Torres • 640
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... Hi Francesco,
Apologies for the delay in answering. I was busy trying to finish a paper myself.
The recount2 project includes base pair coverage BigWig files (see https://f1000research.com/articles/6-1558/v1 for more details on this) that you can leverage to explore any new annotation or un-annota ...
written 4 months ago by
Leonardo Collado Torres • 640
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... RS has a 2nd Windows computer and with a fresh install of R 3.5.1 and Bioconductor 3.8 he got a different error:
R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ...
written 8 months ago by
Leonardo Collado Torres • 640
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