include a viewer for sanger sequencing - scf or ab1 files #890

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1. tnrich commented on Apr 25, 2023

   

   tnrich

   on Apr 25, 2023

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   Hi @jobabi you can already view chromatograms in the editor!

   See here - https://teselagen.github.io/openVectorEditor/#/Editor?searchInput=chr&chromatogramExample=true
2. jobabi commented on Apr 26, 2023

   

   jobabi

   on Apr 26, 2023 via email

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   Hi, thank you for the fast answer. The usual format is .scf or .ab1 for these chromotagram files, which seems not to be recognized by the editor ? Best wishes Jochen From: Thomas Rich ***@***.***> Reply to: TeselaGen/openVectorEditor ***@***.***> Date: Tuesday, 25. April 2023 at 17:16 To: TeselaGen/openVectorEditor ***@***.***> Cc: Christine & Jochen ***@***.***>, Mention ***@***.***> Subject: Re: [TeselaGen/openVectorEditor] include a viewer for sanger sequencing - scf or ab1 files (Issue #890) Hi @jobabi you can already view chromatograms in the editor! See here - https://teselagen.github.io/openVectorEditor/#/Editor?searchInput=chr&chromatogramExample=true — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>
3. tnrich commented on Apr 27, 2023

   

   tnrich

   on Apr 27, 2023

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   @jobabi ab1 files are recognized by the editor:
   

   Just drag an ab1 file into the editor to see
4. jobabi commented on Apr 28, 2023

   

   jobabi

   on Apr 28, 2023 via email

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   Hi Thomas, This seems not to work for me on MacOS. Neither with the online version nor for the local installed one. I tried Firefox and Safari. Best wishes Jochen From: Thomas Rich ***@***.***> Reply to: TeselaGen/openVectorEditor ***@***.***> Date: Thursday, 27. April 2023 at 20:07 To: TeselaGen/openVectorEditor ***@***.***> Cc: Christine & Jochen ***@***.***>, Mention ***@***.***> Subject: Re: [TeselaGen/openVectorEditor] include a viewer for sanger sequencing - scf or ab1 files (Issue #890) @jobabi ab1 files are recognized by the editor: Just drag an ab1 file into the editor to see — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>
5. tnrich commented on Apr 28, 2023

   

   tnrich

   on Apr 28, 2023

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   @jobabi Pretty sure it works.. here it is on safari (also on macos):

   Screen.Recording.2023-04-28.at.11.40.09.AM.mov

   Try doing that with this file and see?
   1_pAS0128A_oMB1064_2022-07-20_A09 2.ab1.zip
6. jobabi commented on May 2, 2023

   

   jobabi

   on May 2, 2023 via email

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   Hi Thomas, Thank you for your patience. I have tested it. It is working for your sample and few of mine, but there are several that do not work. I have no clue what is the difference. The files are from the same company and same day. see attachment. Best wishes Jochen [Archive.zip](https://github.com/TeselaGen/openVectorEditor/files/11370471/Archive.zip)
7. tnrich commented on May 8, 2023

   

   tnrich

   on May 8, 2023

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   Hi @jobabi

   It seems that other AB1 parsers are also struggling with the notfine.ab1 file:

   I tried uploading it on the ab1 parser that mine is based off of here https://eamitchell.github.io/ab1ToJSON/ and it didn't work.

   Also the benchling dna uploader doesn't seem to handle it:
   

   I'm not sure why it isn't working exactly but something seems off in the format of the file that is causing the parser to balk
   Here's the error I see in bio-parsers:
   
8. tnrich commented on May 8, 2023

   

   tnrich

   on May 8, 2023

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   Hmm interesting.. seems like snapgene is able to load the notfine.ab1 file..
   

   that being said, it appears that the root cause of this issue is that the file is saved with the incorrect type of ZTR - https://bioinformatics.stackexchange.com/questions/692/how-can-i-convert-scf-trace-files-to-abi-files?newreg=8143db5a01f0446b962a4584e2cf9227