How to calculate the length of gene coding regions in batches

Sometimes we need to know the transcript length. For example, when using RNA-seq to calculate FPKM, in order to accurately evaluate the expression of different genes, we generally use the total number of reads covering the gene/transcript. Divided by the length of the gene/transcript, sometimes we need to know the length of the gene coding region. For example, when using VAAST to evaluate disease-causing candidate genes, some genes always rank high because of their particularly long coding regions (such as TTN). If Taking into account the length of its coding region, the sorting will be more scientific. So how to obtain the length of the gene coding region? This problem seems relatively simple, just add up the length of each exon. For a single transcript, you can query it through NCBI's CCDS database, but a gene has multiple transcripts, and the coding region of each transcript is overlap, so the gene coding region is not a simple addition of the coding regions of each transcript, so it is not easy to accurately obtain the length of the coding region of each gene, and there is currently no ready-made database. After groping on the Internet, you will The relevant methods are summarized as follows for your reference. First download the gene annotation file GTF from the sanger website, ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz. Then use the GenomicFeatures toolkit in R. library(GenomicFeatures)txdb lt; - makeTranscriptDbFromGFF("yourFile.gtf", format="gtf") collects the coding region number of each gene exons.list.per.gene lt; -cdsBy(txdb, by="gene") Use the reduce function to avoid repeated calculations of the overlapping area exonic.gene.sizes lt; - The gene ID generated by lapply(exons.list.per.gene, function(x){sum(width(reduce(x)))}) is the ensemble number , can be converted to gene symbol through -abcc.ncifcrf.gov/db/db2dbRes.php. In addition, Youxia has already processed the length of the coding regions of all human genes. If necessary, you can leave a message on WeChat to request it.

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