Hi,
I hope you can help me again. I'm trying to do the same thing: export from IGB to CorelDraw, but something weird is happening....
When I try importing an old SVG (exported from IGB), everything is working perfectly. Any other SVG is working fine too. However, any of the SVGs I exported recently are not opening properly in CorelDraw (in Chrome they look fine). In the best case scenario, two very long horizontal lines appear. If I do CTRL+U twice, and delete these lines, I'm able to locate a small mirror image of the tracks I was trying to export. I tried this in a few IGB versions, same results. Converting the files to a different format didn't solve the problem. I also have edited the date to remove the question marks.
Any ideas what I can do?
I attached two files - the new one was exported from version 9.1.4, the old one is from 9.0.2.
Thank you
Miriam
Hi Miriam,
I compared the two files and I can't find anything wrong with the new file. I can load both files in Inkscape (I still don't have access to CorelDraw). I also don't think we have made any changes recently to how svg files are created in IGB.
I've attached two files that I would like you to try to load into CorelDraw and tell me if they appear correctly. I took the new igb file you provided, opened it in inkscape, and then saved it through inkscape as an svg. When I compared it to the original file it appears inkscape has updated/changed the svg formatting. The other file was also created from the new igb file you provided. I have removed two long horizontal lines using inkscape and then saved the file as an svg using inkscape.
Let me know if either of these files works for you in CorelDraw, as it may give me some clues as to what the problem may be.
Best,
Nowlan
Hi Nowlan,
Thanks for your prompt answer.
Both of the original files didn't work properly, from both IGB versions. I am attaching now a file which works fine from March (note that it has the question marks in the date stamp, but it still works fine). An additional file I tried (exported during June) didn't work - had the same horizontal line issue.
I tried out the two files you sent - the one with the horizontal lines did the same thing as my original files, and the one without the lines worked as expected (both look fine when opening them Chrome).
I found out that also in my files I can delete the horizontal lines - to do that I decrease the size to 1% of the original, delete the lines, and then increase by 50,000% to get a full A4 image (the mirroring of the image was caused at this step, and not from the file itself). This is a solution, but it requires some effort just to start the editing of the picture... I also noted that the importing takes CorelDraw much more time than usual.
{And maybe you can please help me with another issue - I updated IGB, and now the mRNA track does not appear - see attached picture of the old & new versions - the IGB quick download does not appear in the new version, so I can't select the Araport annotation. This never happened to me, I always had them displayed as defult even after updating}
.
Thank you
Miriam
Hi Miriam,
Just to confirm, the file chr5_w_high__new_igb_EDITED.svg opened correctly in CorelDraw?
Regarding the IGB Quickload not appearing, can you take a screenshot of the Data Sources menu for me? To get there, click the Configure button in the Available Data box. It looks like the IGB Quickload might not be reachable for some reason.
I will keep looking into the svg issue.
Best,
Nowlan
Hi Nowlen,
Yes, it does. Please see the attached screenshot from CorelDraw, as it looks after importing.
I am also attaching the data sources from the new & old versions (the one on the left is the new one).
Thanks again
Miriam
The Araport annotations should still be available through IGB Quickload. It looks like IGB Quickload is available in your screenshots, so I'm not sure why Araport wouldn't show up.
Try refreshing the Quickload connection by clicking Screen Shot 2020-11-18 at 4.04.26 PM.png in the Data Sources menu and then sending me whatever information appears in the IGB console (Help > Show Console). If that doesn't work then you can try resetting preferences to default. This will restart IGB and reset all of the IGB settings to their defaults. Click IntegratedGenomeBrowser > Preferences > Other Options > Reset Preference to Defaults
Hi Miriam,
The problem with the svg seems to be related to IGB including a very long bar in the svg file. For example,in the chr5_w_high__new_igb.svg file, lines 25 and 33,043 specify a thin line from -362347.5 to 622531.5.
I can replicate the issue in IGB by going to Arabidopsis chr1:8,688,527-8,689,303 and loading the graph from the quickload data RNA-Seq > SM > Graph > Pollen, coverage. When I export the image as svg Main View the svg image includes the long lines. This seems to be an issue with IGB drawing the lines in graph tracks that span the entire chromosome. If I remove the graph track from IGB and resave the svg the lines no longer appear. I also tried older versions of IGB back to 8.0.0 and the lines are still present in the graph track, so it does not seem to be related to the version of IGB, but rather the type of data that has been loaded.
I will need to take a closer look at why this is happening and if there is a way for us to remove the lines in the future. It seems like manually deleting the lines from the svg may be the only option for now.
Best,
Nowlan
Hi Nowlen,
Thank you - resetting the preferences solved the missing annotations problem.
The data I am trying to export now is in bigwig format (.bw). I tried exporting now bedgraph format (.bedgraph), and it worked fine (attached).
Based on what you wrote, I deleted some rows from the svg file - I searched for 808080, and deleted tha row and the next 2 (a total of three rows). It now looked almost normal in CorelDraw - the right half of the image is white (no data was lost, it's just a white expansion) which appears in the 'try' svg as well.
I will carry on doing this for now. Thank you very much for your time and efforts!
Best,
Miriam
SVG generated in IGB 9.0.1 (OSX 10.13.6) works correctly in both Adobe Illustrator and Inkscape. CorelDRAW is only available on Windows so I was not able to test.
User could try using Inkscape in the meantime, unless the issue is on their end.
HELP-92had an issue where the user's computer was set to a language with non ASCII characters, leading to IGB outputting invalid SVG files.