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schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
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syri issues #200

Closed MaOrsucci closed 7 months ago

MaOrsucci commented 1 year ago

Hi Syri user, I'm trying to used Syri between 2 pacBio genomes of fungi. There is a huge amount of rearrangement between these two genomes. I'd like to be able to visualize them with Syri, but when I run syri I get warnings and this error:

Reading BAM/SAM file - WARNING - No primary alignment found for reference sequence JAETXR010000012.1. This could mean that the entire chromosome JAETXR010000012.1 is reapeated. Reading BAM/SAM file - WARNING - No primary alignment found for reference sequence JAETXR010000014.1. This could mean that the entire chromosome JAETXR010000014.1 is reapeated. Reading BAM/SAM file - WARNING - No primary alignment found for reference sequence JAETXR010000015.1. This could mean that the entire chromosome JAETXR010000015.1 is reapeated. Reading BAM/SAM file - WARNING - No primary alignment found for reference sequence JAETXR010000008.1. This could mean that the entire chromosome JAETXR010000008.1 is reapeated. Reading Coords - WARNING - Chromosomes IDs do not match. Reading Coords - WARNING - Matching them automatically. For each reference genome, most similar query genome will be selected. Check mapids.txt for mapping used. Reading Coords - ERROR - JAETXS010000003.1 in genome B is best match for two chromosomes in genome A. Cannot assign chromosomes automatically.

Someone can help me with this issue? Thanks.

mnshgl0110 commented 1 year ago

Hi. Are these assemblies at chromosome-level? If so, then are these genomes similar enough to have homologous chromosomes between the two genomes?

MaOrsucci commented 1 year ago

Hi. On mummer plot they look like a mosaic as you can see in the following plot but it’s still the same species and there is homologous between the two genomes

@.***

From: Manish Goel @.> Reply to: schneebergerlab/syri @.> Date: Tuesday, 13 June 2023 at 14:47 To: schneebergerlab/syri @.> Cc: Marion Orsucci @.>, Author @.***> Subject: Re: [schneebergerlab/syri] syri issues (Issue #200)

Hi. Are these assemblies at chromosome-level? If so, then are these genomes similar enough to have homologous chromosomes between the two genomes?

— Reply to this email directly, view it on GitHubhttps://github.com/schneebergerlab/syri/issues/200#issuecomment-1589245704, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BARDZOWCVTRKUBXQ7FYDVS3XLBOONANCNFSM6AAAAAAZEYIQCU. You are receiving this because you authored the thread.Message ID: @.***>

mnshgl0110 commented 1 year ago

Unfortunately, plots are not visible when replying through email.

MaOrsucci commented 1 year ago

This is the plot form mummer. So we have homologs but we have extensive chromosomal rearrangements. plot_mummer_1vs2_maxgap500_mincluster100_720

mnshgl0110 commented 1 year ago

@MaOrsucci On the face of it, these genomes are too diverged and violates the assumptions made by syri, and hence can't be analysed by syri directly.

In fact, it is the first time I have seen such genomes and find them super weird and have quite some questions. I would like to know more about this system. Would you have time for a zoom chat? Maybe, we can come up with some ideas about what to do with this!

MaOrsucci commented 1 year ago

Hi,

So if you are always interested we can plan to zoom. I will explain you more about these genomes.

Best regards,

From: Manish Goel @.> Reply to: schneebergerlab/syri @.> Date: Wednesday, 14 June 2023 at 10:34 To: schneebergerlab/syri @.> Cc: Marion Orsucci @.>, Mention @.***> Subject: Re: [schneebergerlab/syri] syri issues (Issue #200)

@MaOrsuccihttps://github.com/MaOrsucci On the face of it, these genomes are too diverged and violates the assumptions made by syri, and hence can't be analysed by syri directly.

In fact, it is the first time I have seen such genomes and find them super weird and have quite some questions. I would like to know more about this system. Would you have time for a zoom chat? Maybe, we can come up with some ideas about what to do with this!

— Reply to this email directly, view it on GitHubhttps://github.com/schneebergerlab/syri/issues/200#issuecomment-1590734451, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BARDZOVQZ724CI6XSGZ457LXLFZRDANCNFSM6AAAAAAZEYIQCU. You are receiving this because you were mentioned.Message ID: @.***>