I got a few fastq files from RNA-seq experiment and somebody ask me to check the number of reads that come from retroelements L1-ORF1/2p. Is it a simple way to perform blast of the whole fastq file agains the sequence of the elements (instead of align it to the reference genome using hisat/bowtie/bwa etc) and check the number of reads in each sample? I can try a grep but it can take a long time. Thank you for advise.
You are better off with NGS aligners like bwa. Reasons:
1) They would be faster than blast / grep.
2) They are quality aware.
3) grep cannot do a fuzzy search. So reads with sequencing error or polymorphism will not be found with grep. grep is terribly slow for NGS searches unless you optimize the search params and restrict the search to specific LOCALE.
4) It's supereasy to do it! (just index the spliced sequenced and run bwa mem, for example)