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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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
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