search

schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
305 stars 36 forks source link

ERROR - syri:116 - Unequal number of chromosomes in the genomes. #187

Closed Fei5536 closed 1 year ago

Fei5536 commented 1 year ago

Hello, I'm using syri for identification work, but I'm getting this ： WARNING - syri：116 - Chromosomes IDs do not match. ERROR - syri:116 - Unequal number of chromosomes in the genomes. image I viewed the previous post and saw that I have these scaffolds in my file, but I'm still clumsy in dealing with sequences, I don't know how to deal with it, can I get some supports here please ?

mnshgl0110 commented 1 year ago

Have you tried the solutions proposed here?

Fei5536 commented 1 year ago

Thanks for your recovery, I used chroder, generate a new query genome fasta file and a comment anno file, but I don't know how to use them, cause my coords file and delta file are generated using the original ID and I haven't see syri having parameters can use them. I'm trying to realign them now. It would be grateful if you could tell me how to connect chroder and syri

Fei5536 commented 1 year ago

after using chroder, image Error still exists, this is confusing

mnshgl0110 commented 1 year ago

It seems that you are struggling in setting up the initial files. Please read the documentation here https://schneebergerlab.github.io/syri/ Basically, you need to fist ensure that the genome assemblies are at chromosome level. And then that the two genome fasta files have same number of homologous chromosomes. Then you would have to align them and then run syri.

Currently, it is unclear to me what level the genome assemblies are. I also do not understand the figures that you share. So, I cannot suggest the steps that you would need to perform. If possible, I would suggest that you take help of some colleague who have more experience in handling genomic data. Sorry, for not being super helpful.

Fei5536 commented 1 year ago

Hi, thank you so much for answering my question, I made adjustments to the genomic data, but I ran into a new problem. Why does it output many files instead of one syri.out? image

mnshgl0110 commented 1 year ago

These are temporary files and can be ignored (please check the -k parameter from syri). I am closing this issue as the original issue is now resolved. Please start new issues for other questions.