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.
Since you are talking about RNA-seq you want a splice-aware aligner so bwa and bowtie will not suffice. HISAT is a good one, alternatives are STAR and bbmap.
Thank you. I'll try to run it after indexing. By the way is it possible to run bam files against indexed sequence?
Please use
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when responding to existing posts to keep threads logically organized.If you only need a rough idea of the reads that could be from that transcript you may be able to use kallisto or Salmon to do pseudoalignments.
Thanks. Could you please update the link to instructions?
Again. Please use
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when responding to existing posts to keep threads logically organized. I moved your post now.