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Discrepancy between displayed track data and downloaded BigWig data for Battle et al.
25-Mar-2019, 07:14 PM (This post was last modified: 25-Mar-2019 07:32 PM by drivenbyentropy.)
Post: #1
Discrepancy between displayed track data and downloaded BigWig data for Battle et al.
Hello

First off, thank you very much for this great database, it is truly a helpful tool for the community.

I have an observation that I was hoping you could help me resolve which concerns the Battle et al. dataset. When looking at the full "Elongating Ribosomes (A-site)" in the Browser, the displayed values do not seem to match up with the values when downloading this track in BigWig format (Downloads -> Mamal,Human,HG38,Elongating Ribosomes, Global Aggregate, Battle 2015). As an arbitrary example, the value in the Genome Browser for chr8:142664866 is 101, whereas the same position in the bigWig file has value 53.

It would be great if you could help me highlight where my misunderstanding of this issue is.

Thank you very much in advance and all the best.
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26-Mar-2019, 07:51 AM
Post: #2
RE: Discrepancy between displayed track data and downloaded BigWig data for Battle et al.
(25-Mar-2019 07:14 PM)drivenbyentropy Wrote:  Hello

First off, thank you very much for this great database, it is truly a helpful tool for the community.

I have an observation that I was hoping you could help me resolve which concerns the Battle et al. dataset. When looking at the full "Elongating Ribosomes (A-site)" in the Browser, the displayed values do not seem to match up with the values when downloading this track in BigWig format (Downloads -> Mamal,Human,HG38,Elongating Ribosomes, Global Aggregate, Battle 2015). As an arbitrary example, the value in the Genome Browser for chr8:142664866 is 101, whereas the same position in the bigWig file has value 53.

It would be great if you could help me highlight where my misunderstanding of this issue is.

Thank you very much in advance and all the best.

Hi there,

One possible reason for the discrepancy is that the bigWig files are zero-based and the browser display is one-based. If you find that this is not the reason, can you let us know and we will investigate more.

Thanks,
Audrey
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26-Mar-2019, 01:33 PM (This post was last modified: 26-Mar-2019 01:37 PM by drivenbyentropy.)
Post: #3
RE: Discrepancy between displayed track data and downloaded BigWig data for Battle et al.
(26-Mar-2019 07:51 AM)audrey Wrote:  
(25-Mar-2019 07:14 PM)drivenbyentropy Wrote:  Hello

First off, thank you very much for this great database, it is truly a helpful tool for the community.

I have an observation that I was hoping you could help me resolve which concerns the Battle et al. dataset. When looking at the full "Elongating Ribosomes (A-site)" in the Browser, the displayed values do not seem to match up with the values when downloading this track in BigWig format (Downloads -> Mamal,Human,HG38,Elongating Ribosomes, Global Aggregate, Battle 2015). As an arbitrary example, the value in the Genome Browser for chr8:142664866 is 101, whereas the same position in the bigWig file has value 53.

It would be great if you could help me highlight where my misunderstanding of this issue is.

Thank you very much in advance and all the best.

Hi there,

One possible reason for the discrepancy is that the bigWig files are zero-based and the browser display is one-based. If you find that this is not the reason, can you let us know and we will investigate more.

Thanks,
Audrey

Audrey,

Thank you very much for the quick reply. I do not believe this is an indexing issue. This can be exemplified if we look at a 5nt region around the above example on chromosome 8. I am attaching two screenshots corresponding to the browser view centered around position 142664866 which is highlighted in blue, as well as the same region (142664860-142664870) using the table function of the database (the data of which is identical to the BigWig file from what I can tell). You can see that the value range in the former is [0-101] where as the latter is [0-64].

Please let me know if I can provide with any additional information.

Thanks again and all the best.


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27-Mar-2019, 11:01 AM
Post: #4
RE: Discrepancy between displayed track data and downloaded BigWig data for Battle et al.
Hi,

Thanks for the screen shots. Indeed there does seem to be an issue and we will look into it asap and get back to you.

Audrey
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27-Mar-2019, 08:41 PM
Post: #5
RE: Discrepancy between displayed track data and downloaded BigWig data for Battle et al.
Hi again,

Just to let you know that the issue is fixed and thank you again for bringing it to our attention.

Audrey
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27-Mar-2019, 08:44 PM (This post was last modified: 27-Mar-2019 08:45 PM by drivenbyentropy.)
Post: #6
RE: Discrepancy between displayed track data and downloaded BigWig data for Battle et al.
Hi Audrey,

Thank you for letting me know! I am glad I could be of help.

Best
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