Whether I can only use the RNA-seq data to take a cross-species RNA-seq analysis or not

Question

[hepengcheng]

I know someone use RNA-seq, the genome and all protein sequences to carry out the cross-species RNA-seq analysis.their steps are as follows:

1. RNA-Seq quality filtering and mapping.------> they will get a .bam file.
2. Cross-species annotation using RNA-Seq data.------>they get the orthologous genes by Inparanoid and carry out more strict method to get more exact orthologous genes. Finally, they get a .gtf file.
3. Cross-species differential expression analysis.------>they use the Htseq-count software and the data of .bam and .gtf to carry out the cross-species RNA-seq analysis.

I want to carry out a cross-species RNA-data analysis, but I only have the RNA-seq of two species and haven't the genome and all protein sequences. My opinion is as follows:

1. Get the 'transcriptome' by the software of TRINITY.------>I use the data of RNA-seq and the software of trinity to get the 'transcriptome'.

2. Get all protein sequences.------> I use the nr database to get all protein sequences of the 'transcriptome'.

3. Get the orthologous genes.------>I use all protein sequences to get the orthologous genes of two species and carry out more strict method for the 'transcriptome' to get more exact orthologous genes.

4. Cross-species differential expression analysis.------>use the filtered 'transcriptome' to carry out the cross-species RNA-seq analysis.