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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.
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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.Tags: None
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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07-08-2024, 03:19 PM -
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