search

schneebergerlab / syri

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

unequal chromosomes #181

Closed bijendrabio closed 1 year ago

bijendrabio commented 1 year ago

Hello, Curious, if there's a way to deal with two genomes containing unequal number of chromosomes. kindly suggest!

Regards, B

mnshgl0110 commented 1 year ago

If the genome assemblies are at chromosome scale, then you can use fixchr, otherwise if the assemblies are at contig/scaffold level, then you can try chroder

emmannaemeka commented 1 year ago

Hello, Thanks for this tool. I would want to use chroder to create pseudo chromosomes for my genome. I ran this command

chroder -o a9_scaffold ref.fasta a9_spades.fasta -F B a9.bam
it returned this error Error in opening BAM/SAM file. file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False

I then changed to chroder -o a9_scaffold ref.fasta a9_spades.fasta

It returned this error

chroder: error: the following arguments are required: qry

Please what am i not getting right?

mnshgl0110 commented 1 year ago

Answered here: https://github.com/schneebergerlab/syri/issues/185