Comments (7)
bredelings
commented on August 11, 2024
1
Not at the moment.
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bredelings
commented on August 11, 2024
If this is pending the arrival of the -N option, I could look at another branch.
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jnvaughn
commented on August 11, 2024
I have align 5 5MB genomes and get 22 out of 224 blocks with loops. (This occurs with or without -N flag.) All paths contain many re-used segments in forward orientation and therefore form cycles (Interestingly, we never see a segment used more than twice). I could see this cycle behavior being desired - sibeliaz does a good job absorbing tandem repeats in this way - but the pggb result are less obvious. I have attached a few examples. pggb seems to refuse to smooth short, local (but not tandem) repeats creating these odd structures that, by my eye, need to be flattened. Thanks for any advice.
testDuplicates.txt
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ekg
commented on August 11, 2024
I'll check this out. The block merging was causing some issues in looping
regions but these will be resolved with the merge of the hybrid-map branch.
We have been getting pretty nice results for VNTRs with these fixes.
To reduce looping, you'll need to increase -s, increase -p, and increase
-w, -e, and -j. The alignments may not be able to consistently linearize
highly-similar repeats in of a VNTR, because the direct relationships
between the various copies may be ambiguous.
…On Tue, Mar 23, 2021, 20:49 jnvaughn ***@***.***> wrote:
I have align 5 5MB genomes and get 22 out of 224 blocks with loops. (This
occurs with or without -N flag.) All paths contain many re-used segments in
forward orientation and therefore form cycles (Interestingly, we never see
a segment used more than twice). I could see this cycle behavior being
desired - sibeliaz does a good job absorbing tandem repeats in this way -
but the pggb result are less obvious. I have attached a few examples. pggb
seems to refuse to smooth short, local (but not tandem) repeats creating
these odd structures that, by my eye, need to be flattened. Thanks for any
advice.
testDuplicates.txt
<https://github.com/pangenome/pggb/files/6192330/testDuplicates.txt>
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ekg
commented on August 11, 2024
I have also seen some looping in STRs, which could be creating the effect
you're describing. Setting a higher (seqwish) -k can help. But I'll be
looking at this.
…On Wed, Mar 24, 2021, 07:43 Erik Garrison ***@***.***> wrote:
I'll check this out. The block merging was causing some issues in looping
regions but these will be resolved with the merge of the hybrid-map branch.
We have been getting pretty nice results for VNTRs with these fixes.
To reduce looping, you'll need to increase -s, increase -p, and increase
-w, -e, and -j. The alignments may not be able to consistently linearize
highly-similar repeats in of a VNTR, because the direct relationships
between the various copies may be ambiguous.
On Tue, Mar 23, 2021, 20:49 jnvaughn ***@***.***> wrote:
> I have align 5 5MB genomes and get 22 out of 224 blocks with loops. (This
> occurs with or without -N flag.) All paths contain many re-used segments in
> forward orientation and therefore form cycles (Interestingly, we never see
> a segment used more than twice). I could see this cycle behavior being
> desired - sibeliaz does a good job absorbing tandem repeats in this way -
> but the pggb result are less obvious. I have attached a few examples. pggb
> seems to refuse to smooth short, local (but not tandem) repeats creating
> these odd structures that, by my eye, need to be flattened. Thanks for any
> advice.
> testDuplicates.txt
> <https://github.com/pangenome/pggb/files/6192330/testDuplicates.txt>
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <#26 (comment)>, or
> unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AABDQEKYF5VOHMH27HFYQFTTFDWELANCNFSM4TTUNTYQ>
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jnvaughn
commented on August 11, 2024
Thanks very much. pggb seems be doing well on STRs and VNTRs as evidence here and on some other simulated datasets. The issue above is related more to small local repeats triggering a loop. I have looked at one of the examples above in detail using flanking sequence (text file attached). The little bit of loop-triggering homology is shown in red square in attached dotplot. (On side note, block 700 in maf appears to be a spurious indel related to divergence.) All gfas and raw sequences available at https://github.com/USDA-ARS-GBRU/PanPipes/tree/main/testSets/pggb_5_salmonella.
dotplot.pdf
blockContext.txt
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subwaystation
commented on August 11, 2024
@bredelings @jnvaughn do you have more questions? Else I would like to close this one.
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