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meuleman / epilogos

Methods for summarizing and visualizing multi-biosample functional genomic annotations
https://epilogos.net
GNU General Public License v3.0
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only get the statePairs.txt, no starch or score.txt.gz file #10

Closed ykai16 closed 4 years ago

ykai16 commented 5 years ago

Hi,

After successfully run epilogos on the test data, I tried computeEpilogos_minimal.sh on my own data using the S3 mode, but got only the statePairs.txt for each chromosome, no observations.starch, scores.txt.gz or exemplarRegions.txt file. Also no error messages. I checked my input data format and it seems to be exactly the seem with the test data in the epilogo package. So I am now really puzzled..Could you please point out what could be wrong? Thanks.

Yan

erynes commented 5 years ago

Thanks Yan. How many samples / epigenomes do you have, and how large is your input data? Could you also e-mail me an excerpt from your input data? Also, please send the exact command (with all arguments) that you are using to run epilogos.

Eric

ykai16 commented 5 years ago

Hi Eric, Thanks a lot for the quick reply! After carefully looking into my input data, I found this is because the input matrix contains string with numerical vaules in some lines. After remove these strings, epilogos runs properly and output all the expected results.

Here is another issue I had with the visualization of the qcat files using the old WashU genome browser. I followed the steps in the qcat.md to create the files, but found that WashU cannot display the track (please see the screen shot below). Could you help look at the files and point what could be wrong? The files I used can be seen in this dropbox link:https://www.dropbox.com/sh/gdcpl9jfn8yp0kk/AACi33539cWIIXhXliaTi9BCa?dl=0

Thanks, Yan

Screen Shot 2019-11-11 at 12 04 42 PM
erynes commented 5 years ago

Hi Yan, I'm glad to hear that it's working for you now. Thanks for including your input files and that browser shot in your reply. That browser shot shows a region on chr7; the input you shared only contains data for chr1. Could this be the problem? If you specify a region on chr1, does the data display properly for you?

Eric

On Mon, Nov 11, 2019 at 9:08 AM ykai16 notifications@github.com wrote:

Hi Eric, Thanks a lot for the quick reply! After carefully looking into my input data, I found this is because the input matrix contains string with numerical vaules in some lines. After remove these strings, epilogos runs properly and output all the expected results.

Here is another issue I had with the visualization of the qcat files using the old WashU genome browser. I followed the steps in the qcat.md to create the files, but found that WashU cannot display the track (please see the screen shot below). Could you help look at the files and point what could be wrong? The files I used can be seen in this dropbox link: https://www.dropbox.com/sh/gdcpl9jfn8yp0kk/AACi33539cWIIXhXliaTi9BCa?dl=0

Thanks, Yan

[image: Screen Shot 2019-11-11 at 12 04 42 PM] https://user-images.githubusercontent.com/16323164/68606034-8bbb0700-047b-11ea-803a-a286a0b2b565.png

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ykai16 commented 4 years ago

Hi Eric, Thanks for pointing that out! This is indeed the reason. The default region for WashU browser is chr7 and the centromere region of chr1, so I thought there is no signal... Thanks for the help!

Yan

erynes commented 4 years ago

Hi Yan, I'm glad to hear there wasn't any issue. Thanks for using Epilogos. If any more questions come up, please let us know, we're here to help.

Eric