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  • calculate FPKM for specific region

    Hi, all,

    I am trying to get FPKM value for specific region(UTR, exon, or even partial exon). i tried to generate my own GTF file include only information for my interesting region, however, the CUFFLINKS result is empty. i also tried to count reads using this GTF file from HTSEQ, and the results is still empty. is there something wrong with my GTF file or this way wont work anyway?
    Last edited by zjrouc; 07-29-2015, 02:26 PM.

  • #2
    Are the fields in your GTF file tab separated (http://www.ensembl.org/info/website/upload/gff.html)?

    As Devon asked in your other thread (http://seqanswers.com/forums/showthread.php?t=61541) have you checked the region in IGV (or a similar browser) to verify that there are indeed reads aligning in that region.

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