include a viewer for sanger sequencing - scf or ab1 files

[jobabi]

Hi, what about the idea to add an viewer for sanger sequencing results? maybe one of these could be implemented ?

https://github.com/y9c/cfutils https://github.com/labsquare/CutePeaks https://github.com/topics/sanger-chromatograms

best wishes

Jochen

@tnrich

[tnrich]

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

See here - https://teselagen.github.io/openVectorEditor/#/Editor?searchInput=chr&chromatogramExample=true

[jobabi]

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

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[tnrich]

@jobabi ab1 files are recognized by the editor:

Just drag an ab1 file into the editor to see

[jobabi]

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

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[tnrich]

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

https://user-images.githubusercontent.com/2730609/235227769-a7bb9fdd-b3f7-4166-94a1-48b17e35ea6e.mov

Try doing that with this file and see? 1_pAS0128A_oMB1064_2022-07-20_A09 2.ab1.zip

[jobabi]

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

[tnrich]

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:

[tnrich]

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