MAKER: how to use RNAseq data to assist annotation?

Question

[bbscience]

Hello,

I am performing a MAKER annotation of a de novo plant genome. I have RNA sequencing reads (Illumina paired-end 150bp) to include in the annotation. However, I am confused about the inputs MAKER allows in the maker_opts.ctl file. I performed a Trinity genome-guided (my de novo genome assembly) transcriptome assembly and have the trinity.fasta file. Where do I input the .fasta transcripts file in MAKER? Can I use the RNA seq data in any other way? Should I use closely related organism ESTs and Proteins from NCBI and align it to my genome to provide .gff files? I am confused between the difference of ESTs and RNAseq.

Thank you for any advice and assistance! Cheers

maker_opts.ctl

#-----EST Evidence (for best results provide a file for at least one)
est= #set of ESTs or assembled mRNA-seq in fasta format
altest= #EST/cDNA sequence file in fasta format from an alternate organism
est_gff= #aligned ESTs or mRNA-seq from an external GFF3 file
altest_gff= #aligned ESTs from a closly relate species in GFF3 format

#-----Protein Homology Evidence (for best results provide a file for at least one)
protein=  #protein sequence file in fasta format (i.e. from mutiple organisms)
protein_gff=  #aligned protein homology evidence from an external GFF3 file

Answer 1

[Juke34]

If you have you transcriptome in fasta format (as it must be for Trinity) then:

est=path_to_my_trinity_assembly1.fasta, path_to_my_trinity_assembly2.fasta

If you have other transcriptome of your species in gff format you can also use:

est_gff=transcriptome1.gff,transcriptome2.gff

If your transcriptomes are not species specific then you should use alt_est instead of est and altest_gff instead of est_gff parameters. (It will use mapping with less constraints )