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  • Tophat Junction reads are very low comapred to ERANGE

    Does any one know why the number of junction reads of TopHat (117410) are very less compared to ERNAGE. It should be more than ERANGE I suppose ?

    And the genomic reds number is more than the original reads? (32233301)

    I ran Illumina solexa single end rnaseq reads

    BLAT+ERANGE
    Samples No. Reads Genomic reads Genomic reads Junction reads
    Adipose 27752231 17.6 M (unique) 4.8 M (non-unique) 1.4MB


    BOWTIE+TOPHAT

    Samples No. Reads Genomic reads Junction reads
    Adipose 27752231 32233301 117410

  • #2
    Could you give us a bit more information about how you count the number of reads?

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