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  • rururara
    Member
    • Jan 2011
    • 31
    #1

    tophat-mining SNP

    anyone who has experience use TopHat to analyse data from RNA seq?
    i have 2 questions here.

    1. Which output file in TopHat can be used to mining SNPs
    using SAMTools. Is that acceptedhits.bam?
    i'm a beginner in analyzing RNA seq so there's a liltle bit confuse for me to understand the output from TopHat. Infact I'm using RNA seq to mining the SNPs.

    2.what also we can do with junctions.bed data? do we need to map back the unmapped reads from bowtie to junctions.bed?
    thanks!
    Tags: None
  • honey
    Senior Member
    • Feb 2010
    • 151
    #2
    This thread may help you to get you what you are looking there are other tools to take Bam file of TOpHat.
    RNAseq: Pipeline to detect allele specific expression - SEQanswers
    http://seqanswers.com/forums/showthread.php?t=6148&highlight=RNASeq
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

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