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Initiating ribosomes global aggregate data
17-May-2019, 01:55 PM
Post: #1
Initiating ribosomes global aggregate data
It looks like the global aggregate track for initiating ribosomes is no longer available to download in bigWig format. Is there any other location this data can be downloaded from? Have these data been updated since March 2018? I have a bigWig file that was downloaded around that time and the numbers I see in my file do not match the ones I see in the genome browser.
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17-May-2019, 02:46 PM
Post: #2
RE: Initiating ribosomes global aggregate data
Hi,

The reason that a single global aggregate track is no longer generated is that computationally it was taking more and more time to generate (more so with the elongating ribosome profiling data) and we decided instead to change our pipeline and make use of the in-built functionality to stack tracks which generates a single track for exploration. We realise that this has its drawbacks and apologies that it has caused you inconvenience.

Regarding differences between numbers, the Zhang 2017 data was added in mid Februrary 2018 for hg38. Could this account for the differences?

If not, could you send an example that differs from your bigWig so that we can explore more?

Kind regards,
Audrey
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17-May-2019, 03:07 PM
Post: #3
RE: Initiating ribosomes global aggregate data
Thank you for the quick response!

Based on the file name (Global_RiboProInit.19_02_2018.bw), I think it includes data from Feb 2018.

Example case where the bigWig I have differs from the browser:
Code:
## convert bigWig to bedGraph
$ ./UCSCTools/bigWigToWig Global_RiboProInit.19_02_2018.bw Global_RiboProInit.19_02_2018.bedgraph

## find a specific region in chromosome 3
$ grep '^chr3' Global_RiboProInit.19_02_2018.bedgraph | awk 'BEGIN{FS="\t";OFS="\t"}($2>51975265 && $3<51975275)'
chr3    51975269        51975270        3
chr3    51975270        51975271        432
chr3    51975271        51975272        25

The exact same region seen in the browser: http://bit.ly/2Qb8LXA
Note the 'Initiating ribosome profiles from all studies' track tops at 36 reads instead of the expect 432 (based on what's in the Global_RiboProInit.19_02_2018.bw file)
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23-May-2019, 08:22 AM
Post: #4
RE: Initiating ribosomes global aggregate data
Hi,

Unfortunately there does indeed seem to be an issue. We have checked the Global_RiboProInit.19_02_2018.bw file and it corresponds to what you report for the region chr3:51975269-51975272.

It is difficult to determine why there is such a discrepancy in the counts with the current Global Initiating Ribosomes track unless an error had been made when merging the files for the previous approach.

We will try to find an explanation and let you know as soon as we can.

Apologies again,
Audrey
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