mapping and de novo assembly of plant without reference genome

Question

[snstab]

Hi I'm studying on a plant that has no reference genome and only has one scaffold assembly and one gff3 annotation file. Can I create an index with the same assembly and gff3 in STAR and do the mapping? If I want to do de novo assembly using the Galaxy Can I import the links of 20 fastq files from the RNA-seq of the samples together to construct the Reference Genome with Trinity? If this is possible, please help me import the links of these files together into Galaxy and make the reference genome.

Thanks a lot

Answer 1

[andres.firrincieli]

Hi,

Can I create an index with the same assembly and gff3 in STAR and do the mapping?

You can definitelly do that but in your case I would go for the option number 2: use the fastq files to assemble the transcriptome

please help me import the links of these files together into Galaxy and make the reference genome.

I never used Trinity from Galaxy but it has is own suppor forum: link. You could ask there for assistance