the question is not very clear, but I'll just give it a go.

fastq is a file format only for unmapped reads. if you need contig details then you would have to map those reads first. unless you have fastq files with reads coming only from a particular contig, in which case you would be the only one knowing with contig they've been sequenced from, and I guess that would be the information you need.

if your intention is to submit RNAseq data to SRA, there's a SEQanswers' thread that may be of your interest.