baoxingsong/AnchorWave

How to align between contig genome and chromosome genome?

Yujiaxin419 opened this issue · 3 comments

Yujiaxin419 commented

Dear Dr. Song,

Thanks for developing this useful tool.

We are trying to align a tetraploid contig level genome to the tetraploid chromosome-scale genome, using anchorwave proali function. The two genome are the same species, which has undergone two whole genome duplication events in evolution. However, only partially contigs (~35%) can be align to reference genomes using proali.

I've extracted coding sequence using anchorwave gff2seq command from GFF file and FASTA file of reference genome, mapped the genome onto coding sequence to generate the two SAM files, and using the following parameters for anchorwave proali command:

anchorwave gff2seq -r ${ref} -i ${gff} -o cds.fa -m 0
minimap2 -x splice -t 20 -k 12 -a -p 0.4 -N 20 ${qry} cds.fa > cds.sam
minimap2 -x splice -t 20 -k 12 -a -p 0.4 -N 20 ${ref} cds.fa > ref.sam
anchorwave proali -i ${gff} -as cds.fa -r ${ref} -a cds.sam -ar ref.sam -s ${qry} -n anchors -m 0 -R 1 -Q 1 -t 20 -o alignment.maf -f alignment.f.maf

Do you have any idea about why only partially contigs can be aligned and how to increase the alignment rate in this case.

Thanks a lot,
JiaxinYu

baoxingsong commented

Could you share the summary information of your assemblies and annotation, please?
Or share your files if it is possible.

Yujiaxin419 commented

Hello Dr. Song,

I originally intended to send a test data set to your email song@mpipz.mpg.de. But it rejected by the server. Could you please give me an email address that can be delivered?

Thanks for your help.

Jiaxin Yu