I',m working with the wolf genome and want to retrieve a specific region. The ENA only provides me the FASTQ file http://www.ebi.ac.uk/ena/data/view/ERS715549. If i had the SAM file i could simply use samtools to retrieve the specific region given a BED format. However starting from the FASTQ I`m not sure what to do. I believe that to do so I need first to index the genome reference from canFam3 with BWA or Bowtie2, align the whole wolf genome with the canFam3, convert to SAM and then retrieve the sequence of interest. Is that right? Or there is an shorter path to work?