Multispecies fastq file - identification of SNP

Question

[tomeksilentfall]

Hello everybody,

I have few fastq files which contains two fish species with two different tissues (these fish are from different families).
I would like to know if it is possible to assign gene abundance to each species or better say what gene is expressed by which fish based on SNPs? Both fishes have available genomes.

I am aware that for many genes it will not be possible. However, I believe there will be also some specific genes because of tissue specifity.

Thank you for answers.

EDIT: I am sorry but to say it more precisely: Each fish has sequenced different tissues (not each fish has two tisssues).

[colindaven]

Have you got RNA-seq or WGS data ? What have you tried so far?

If RNA-seq, have you tried mapping the reads to the respective genomes and quantifying ? Do the genomes have gene annotations ?