I study variant analysis of Pseudomonas aeruginose illumuna sequence. My workflow:
1-FastaQC read quality reports - R1,R2 wildtype
2-trimmomatic (SLIDINGWİNDOW (4:30)
3-Snippy variant analysis with reference sequence ( by adding fna and gff file)
finalyy, I use JBrowse interactive visualisation.
However, I can only observe the reference genome in my JBrowse output. I can’t see my wildtype and other entries. (I’ve attached my JBrowse output screenshot)
can you help me with this?
(Snippy and JBrowse illumina sequences not working?))
Overall, the screenshot is showing that none of the data in the files “overlaps” with the genome coordinates. Looking closer, it seems the NC accession sequence used for the genomic sequence is a mismatch for the NC accession sequence the data is based on.
Different accession sequences will use different coordinate systems, which probably explains what is going on. Try viewing the data against the NC accession sequence used for all the other steps. You already have a copy of that, correct? See Reference sequence NCBI ID number - #2 by jennaj