Liftover fails for several regions

[Emma]

Hi! Why is this liftover failing? Is there a workaround? I'm mapping from hg38 to hg19. 

Thank you!

#Split in new
chr1 145686997 148411223
#Split in new
chr1 145686997 148411223
#Split in new
chr1 145808272 148411223
#Split in new
chr1 145808272 148411223
#Split in new
chr10 46005406 49845537
#Split in new
chr10 46005406 49845537
#Split in new
chr15 22782170 28134728
#Split in new
chr15 22782170 28134728
#Split in new
chr15 22782170 30076787
#Split in new
chr15 22782170 30076787
#Split in new
chr15 22782170 32153204
#Split in new
chr15 22782170 32153204
#Split in new
chr15 82534140 85169770
#Split in new
chr15 82534140 85169770
#Split in new
chrX 48447780 52444264
#Split in new
chrX 48447780 52444264

[Emma]

If I set Minimum ratio of bases that must remap: 0.9, then I'm able to liftover several of them. However, 3 remain:

#Split in new
chr1	145686997	148411223
#Split in new
chr1	145808272	148411223
#Split in new
chr10	46005406	49845537

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[Matthew Speir]

Hello, Emma.

Thank you for your question about LiftOver.

These final three regions are fairly large and appear to have changed quite significantly between hg19 and hg38. Here is a session showing your first region in hg38 with the "Hg19 Diffs" and "LiftOver" tracks displayed: https://genome.ucsc.edu/s/mspeir/hg38_LiftOver_37309. Red items in the "Hg19 Diffs" track indicate new sequence contigs in the hg38 assembly. 

You may have better luck attempting to lift these regions by splitting them into smaller segments or by checking the box "Allow multiple output regions" in the LiftOver tool.

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.

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Matthew Speir

UCSC Genome Browser, User Support

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[Emma]

Thank you!

May I ask you how did you import these overlaps to UCSC browser? Thanks again :) 

[Gerardo Perez]

Hello, Emma.

Thank you for your follow-up question.

To import these overlaps into the UCSC Genome Browser, you can load your regions as a Custom Track:

1. Go to the Custom Tracks page for hg38: https://genome.ucsc.edu/cgi-bin/hgCustom?db=hg38 (also found under "My Data" > "Custom Tracks" in the blue bar menu).
2. Paste your regions in BED format into the text box, for example:

chr1 145686997 148411223                    
chr1 145808272 148411223                                                                                                                                                                                                                             
chr10 46005406 49845537

3. Click "Submit". You'll be taken to the Manage Custom Tracks page. From there, click "Go to first annotation" to view your regions in the genome browser.

In the session Matt shared previously, he also turned on two additional tracks set to "pack" to help illustrate why the liftOver was splitting:

LiftOver & ReMap - shows alignments from hg38 to the hg19 genome assembly, used by the UCSC liftOver tool and NCBI's ReMap service. More information: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=liftHg19
Hg19 Diff - shows the differences between the hg38 and hg19 assemblies, indicating contigs (or portions of contigs) that are new to the hg38 assembly. More information: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=hg38ContigDiff

You can find these under the "Mapping and Sequencing" track group on the browser graphic page and set their visibility to "pack".

I hope this helps. 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.

Gerardo Perez
UCSC Genomics Institute

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/aa7c04cc-ad24-43ba-994a-bf2120611442n%40soe.ucsc.edu.