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  • #1

    questions for tophat

    In tophat paper, for the seed-and-extend strategy to map IUM reads, there is a paramter k to control the index length of reads. Tophat try to find and reads that span splice junctions by at least k bases on each side.The default value for k is 5 in the paper.
    However, when i use tophat (v1.0.12), I always get spliced reads having 3bp length in one side of junction. How to explain the output?
    How to change the default value for k in command line tophat?
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