Hello community!
My name is Stefany, currently in Costa Rica. As a result of my PhD we annotated a genome using the Braker pipeline. Therefore we have a manuscript ready to submit. However after submitting the WGS assembly to the NCBI I came across with some issues. I don't know well how to solve them (know what need to accomplish but don't know how) and was wondering if anyone could give me a heads up to see if can get this paper out of my way. The issues are two: 1) I have 4 genes which have an X on the amino acid sequence, meaning this could be any amino acid 2) I have few genes which are spliced forms and the way to fix this is by including a note as follow: note alternatively spliced
I'm using this command to create my *.sqn file: ./table2asn_GFF -M n -J -c w -euk -t template.sbt -gaps-min 10 -locus-tag-prefix EX895 -l paired-ends -j "[organism=XXX XXX] [isolate=XXX]" -i Genome_PGRAM_editedTosubmit.fsa -f PGRAM_to_Submit_gtf.gff -o PGRAM_to_Submit.sqn
Where should I include the note "alternatively spliced" for all the isoforms? on the Braker output gff file or on the *.sqn file? I'm not sure how to solve this, got to far to quit, any one please some ideas?
Thank you!!
