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  • crazyhottommy
    replied
    check here:http://genomewiki.ucsc.edu/index.php..._or_gff_format

    Leave a comment:


  • cnyh
    replied
    That does look very helpful indeed. Thanks for the tip!

    Leave a comment:


  • iris_aurelia
    replied
    Why don't you give HTSeq-count a try? It takes a GTF file and a sam file as an input and outputs counts per gene for each gene in the GTF file.

    Leave a comment:


  • cnyh
    started a topic GTF file with one line per gene?

    GTF file with one line per gene?

    I would like to use bedtools to extract raw gene counts from my .bam files. However, I was using UCSC_Genes.gtf (human) as my source file, but that file contains multiple lines for each gene, which is an issue since the output from bedtools is in the same format.

    Where can I find a .gtf file containing only a single line for each gene? Preferably with Entrez gene IDs if this is easily available.

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    Multiomics Techniques Advancing Disease Research
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    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

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