bed file for sequences aligned on the reference genome

[uggulhan]

Hi,
I have produced ragoo.fasta file with using soapdenovo2 assembly as the input and a reference genome with its gff file. The command is below:
ragoo.py genome.fasta ref_genome.fna -m minimap2-master/minimap2 -gff genomic.gff -b -s -C
According to assembly statistics, nearly half of the assembled genome is aligned to reference genome. I want to use the new reference based oriented ragoo.fasta as the reference genome for variant calling analysis of a sample fastq file. However, when I used ragoo.fasta directly, variant coordinates differ according to original reference genome (ex. I have 200000 bases for 1 contig in ragoo.fasta, however there are 300000 bases for the same contig in original reference genome/assembly). Thus I need a bed file for aligned regions, which I can use in variant calling analysis.
Even I have used -s flag in my code, no bed file was produced under pm_alignments folder. There is just contigs_against_ref.paf file, can I convert this file into bed file, to be used in variant calling analysis?
I look forward to your comments on this,
Best Regards..

[malonge]

Hi there,

I apologize for my delayed response.

First of all, I recommend switching your analysis over to RagTag, if at all possible:

https://github.com/malonge/RagTag

Though ragtag is much improved over RaGOO, I think your question will remain the same. And just so that I understand, are you curious to see I you can "lift-over" or "project" variant calls with respect to the reference onto the new ragoo scaffolds?

Thanks,
Mike