I am trying to use StringTie with a reference annotation from my history but get a warning "no reference transcripts were found for the genomic sequences where reads were mapped! Please make sure the -G annotation file uses the same naming convention for the genome sequences".
I downloaded both the reference annotation "Bdistachyon_314v3.1.gene.gff3" and the reference genome I have used the for HiSat2 alignments "Bdistachyon_314v3.1.cds.fa" from the same genome version in Phytozome. I read on another post to check the chromosome names using BAM to SAM and get:
QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT
@HD VN:1.0 SO:coordinate
@SQ SN:Bradi0180s00100.1 LN:1047
@SQ SN:Bradi2g20400.1 LN:1440
While my gff3 file looks like:
Seqid Source Type Start End Score Strand Phase Attributes
gff-version 3 annot-version v3.1 species Brachypodium distachyon
Bd1 phytozomev10 gene 10581 11638 . + . ID=Bradi1g00200.v3.1;Name=Bradi1g00200;...
Bd1 phytozomev10 mRNA 10581 11638 . + . ID=Bradi1g00200.1.v3.1;Name=Bradi1g00200.1;...
Bd1 phytozomev10 CDS 10581 10850 . + 0 ID=Bradi1g00200.1.v3.1.CDS.1;Parent=Bradi1g00200.1;....
I'm not sure what I should be doing to make these compatible. Any ideas?
Best wishes from a newbie, s