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  • Comparing Multiple junctions.bed files from Tophat

    Hi,

    I was wondering if anyone has any experience comparing junctions.bed files from tophat runs across multiple libraries. Basically I would like to see which junction is being "expressed" and "not expressed" across multiple libraries. I've used the parameter --no-novel-juncs so that it doesn't look for novel junctions and only tries to search for reads across known junctions supplied by a refseq.gtf file (which I downloaded from UCSC).

    My original though was that this should give a consistent junction feature set across all libraries so that I can compare against them easily. But it seems that Tophat doesn't report junctions that have no reads (correct me if I am wrong) and the junction IDs, from the junctions.bed file, are only relevant within the its own file (in other words, the IDs do not transfer across junctions.bed files).

    Has anyone else tried to do something like this before? Any help/advice would be appreciated.

    Thanks,

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