Lift Genome Annotations - Format Issues

[Mireya Morote Faubel]

ear Sir/Madam,

I am writing you because I have been trying to use the the tool "Lift Genome Annotations" from Genome Browser but very unsuccesfully. My problem is that I can make the conversion of my variants but without any name tags on them, the moment I try to add a fourth column, following the BED format, as the name of the line (in this case, my variants), all the conversions fail. I have tried using headers but at this moment nothing has worked and I really need help, because it is really useless to have the conversions if I do not know to which of my variants each one corresponds. In addition, I have to say that the problem exists because not all of my variant have a succesful conversion, from 39.684, only 38.234 are converted and 1.450 fail. This is another problem because I don´t know why these one cannot be converted from hg38 to hg19. I hope you can help me. Thank you very much.

Sincerely,

Mireya Morote

PS: I´m attaching an example of what I wrote. 

Mireya Morote Faubel, PhD student

Accredited Research Group of Hematology and Hemotherapy
Health Research Institute Hospital La Fe (IIS La Fe)
Lab 4.06, floor 4, tower A
Avda. Fernando Abril Martorell, 106
CP.46026, Valencia
Telf. +34 9612244737

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[Jairo Navarro Gonzalez]

Hello,

Thank you for using the Genome Browser and sending your inquiry.

LiftOver failed since the BED input was in 1-based coordinates (e.g. chr1 300 300) and most of our tools require the zero-based coordinates (e.g. chr1 299 300). BED coordinates like your example must be 0-based (the first position of chr1 is 0). If you subtract one from each start coordinate you shared with us, each position lifts successfully.

You should be able to automatically subtract one from each start position with the following UNIX command:

awk '{print $1, ($2=$2 - 1), $3, $4, $5, $6}' oldFile > newFile 

For more information about 0-based vs. 1-based coordinates, please see the following blog post:

http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

Want to share the Browser with colleagues?
Host a workshop: https://bit.ly/ucscTraining

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[Mireya Morote Faubel]

Mireya Morote Faubel, PhD student

Accredited Research Group of Hematology and Hemotherapy
Health Research Institute Hospital La Fe (IIS La Fe)
Lab 4.06, floor 4, tower A
Avda. Fernando Abril Martorell, 106
CP.46026, Valencia
Telf. +34 9612244737

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De: Mireya Morote Faubel <mireya...@iislafe.es>
Enviado: lunes, 26 de abril de 2021 16:03
Para: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Asunto: RE: [genome] Lift Genome Annotations - Format Issues

 

Hello,

I´ve been able to run the conversion but I have 1450 variants that resulted in an error. I´m attaching a file with those variants. We´ve checked with our annotated variants in hg38 and those variants that cannot be converted are located in intergenic regiones, so maybe they correspond to a "gap" in the genomic information stored in the hg19 genome. Do you think you could give us some advice of how to convert these variants or if it is even possible due to this possible gap in the information? Thank you.

Sincerely,

Mireya

Mireya Morote Faubel, PhD student

Accredited Research Group of Hematology and Hemotherapy
Health Research Institute Hospital La Fe (IIS La Fe)
Lab 4.06, floor 4, tower A
Avda. Fernando Abril Martorell, 106
CP.46026, Valencia
Telf. +34 9612244737

---

De: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Enviado: viernes, 23 de abril de 2021 3:01
Para: Mireya Morote Faubel <mireya...@iislafe.es>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Asunto: Re: [genome] Lift Genome Annotations - Format Issues

 

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[Brian Lee]

Dear Mireya,

Thank you for using the UCSC Genome Browser and your question about coordinates that do not map from hg38 to hg19.

The reason these coordinates do not map is that they fall into regions of the assembly that are classified as a "New contig added to hg38 to update sequence or fill gaps present in hg19."

Here is a quick session to load that will show just three of the coordinates and the genome sliced in our Multiregion mode to so you can see them side-by-side with a track called "Hg19 Diff" below showing red blocks.
http://genome.ucsc.edu/s/brianlee/hg38_hg19_lift_Deleted_in_new

If you click into the red blocks you can find the track description helping explain the colors and a link to Genbank for more information.

Here is another session with a single red highlight representing where one of your items are located. This session also shows how these items fall in red "New contig added to hg38 to update sequence or fill gaps present in hg19" and also has related alignment tracks shown that help demonstrate how hg38 maps to hg19: http://genome.ucsc.edu/s/brianlee/NewHg38

In the end liftOver does not return results for these regions because hg19 and hg38 are not exactly the same and these regions are ones that researchers need to examine more closely in terms of their research.

Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/DB7PR06MB4604EAAF873129781F33BBFAE5419%40DB7PR06MB4604.eurprd06.prod.outlook.com.

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Brian Lee

UCSC Genome Browser  

UC Santa Cruz Genomics Institute |  Revealing life’s code.

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