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  • How to query microsatellites in a set of data

    Hi everyone,

    I have randomly selected a small subset of microsatellites from a large group of repeat motifs that I found in a set of sequenced dna, using Phobos.
    I now want to find out if the same sequences in the subset are present in a different set of data i.e. I want to query them in this other different set of data.

    How would I go about doing that? What suggestions would you give?
    Thanks in advance

  • #2
    for a simple high-level query use grep in linux

    eg

    grep YOURREPEAT file.fastq
    grep YOURREPEAT file.fastq > output.file
    grep -c YOURREPEAT file.fastq

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