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  • Dixi06
    Junior Member
    • Aug 2017
    • 1
    #1

    splitting Tophat2 bam files in separate samples

    Hello everyone,

    I have RNA seq data of 12 samples (paired end, so 24 files) and I ran tophat2 for alignment on all of them which gave me one bam file for all the samples. Now I need separate bam files for all the samples. Can I spilt them from the one I have or I have to do tophat2 for all the samples separately? If yes, how to do it.

    I need them for FRASER (spilicing detction) I would also appreciate if anyone used FRASER before could help me a bit to get started. I am working with plant data for the first time.

    Thanks.
    Tags: fraser, plant_sequence data, rna sequencing, splicing, tophat2
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