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  • targeted resequencing data analysis tool

    Hi,

    What tool would you recommend for aligning/assembling data obtained from targeted sequencing (Illumina paired-end) of a gene of interest (species is homo sapiens) from different samples?

    Appreciate any suggestions or feedback?

    Regards,
    BD

  • #2
    Lacking further details, I would presume that simply aligning with whatever aligner you normally use (bowtie2, bwa, novoalign, etc.) would do what you want. If this is from a capture experiment, you might want to align to the whole genome to decrease incorrect mappings (assuming that this is important for you, which I'm going to guess it is).

    Comment


    • #3
      Yup. Align to the whole genome. Later, if you want, you can filter the .bam to only include the targeted region.

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