Dear Biostar community,

I have a question regarding use of ragtag to update gene annotation.

I have a scRNA-seq data which is generated using a cultivar for which gene annotation (gff or gtf files) are not available. I have my_cultivar_ragtag.scaffold.fasta, my_cultivar_ragtag.scaffold.fasta.fai, my_cultivar_p_ctg.fa, my_cultivar_p_ctg.fa.fai files for the cultivar that was used foe experiment, but not gtf or gff files. On the other hand, I have reference genome and annotation for another cultivar (reference).

I used

ragtag.py scaffold my_cultivar_ragtag.scaffold.fasta reference.fa -o ragtag_scaffold ragtag.py updategff reference.gff3 ragtag_scaffold/ragtag.scaffold.agp > updated_ragtag_scf.gff3

Then used I used ragtag_scaffold/ragtag.scaffold.fasta and updated_ragtag_scf.gff3 for indexing and mapping with cell ranger, however the reads mapped to the genome remains below 40% (usually >90%).

I will be grateful if someone answer how to correctly use ragtag in this case or in general how to deal with a situation when "same" genome annotation/reference genome is not available but draft genome assembly is available.

Thanks in advance, RS