可以用的着，在biostar https://www.biostars.org/p/77188/ 找到的解答。记录留存一下，不一定要用，参考解决思路
It's not that easy. The GTF only has a feature category called UTR. The end user has to figure out if it is a 5' or 3' UTR. Here is a reproducible example in R of categorising them. Note that some protein-coding transcripts have a 5' UTR and no 3' UTR, a 3' UTR and no 5' UTR, or have neither UTR. It is important to remember the GENCODE annotation is a collection of transcript fragments, not full-length models.
library(GenomicRanges) # From Bioconductor.
genes <- read.table("gencode.v17.annotation.gtf", sep = '\t', skip = 5, stringsAsFactors = FALSE)
whichCodingTranscripts <- genes[, 3] == "transcript" & grepl("transcript_type protein_coding", genes[, 9], fixed = TRUE)
proteinTranscripts <- genes[whichCodingTranscripts, ]
strands <- proteinTranscripts[, 7]
allFeaturesTranscripts <- gsub("transcript_id ", '', sapply(strsplit(genes[, 9], "; "), '[', 2))
proteinTranscriptsNames <- allFeaturesTranscripts[whichCodingTranscripts]
whichCDS <- genes[, 3] == "CDS" & allFeaturesTranscripts %in% proteinTranscriptsNames
transcriptsCDS <- genes[whichCDS, ]
transcriptsCDS <- split(GRanges(transcriptsCDS[, 1], IRanges(transcriptsCDS[, 4], transcriptsCDS[, 5]), transcriptsCDS[, 7]),
factor(allFeaturesTranscripts[whichCDS], levels = proteinTranscriptsNames))
firstCDS <- mapply(function(CDS, strand) {if(strand == '+') {CDS[1]} else {CDS[length(CDS)]}}, transcriptsCDS, strands)
lastCDS <- mapply(function(CDS, strand) {if(strand == '+') {CDS[length(CDS)]} else {CDS[1]}}, transcriptsCDS, strands)
whichUTR <- genes[, 3] == "UTR" & allFeaturesTranscripts %in% proteinTranscriptsNames
transcriptsUTR <- genes[whichUTR, ]
transcriptsUTR <- split(GRanges(transcriptsUTR[, 1], IRanges(transcriptsUTR[, 4], transcriptsUTR[, 5]), transcriptsUTR[, 7]),
factor(allFeaturesTranscripts[whichUTR], levels = names(firstCDS)))
transcriptsUTR5 <- mapply(function(UTR, CDS, strand)
{
if(strand == '+') UTR[UTR < CDS[1]] else UTR[UTR > CDS[length(CDS)]]
}, transcriptsUTR, firstCDS, as.list(strands), SIMPLIFY = FALSE)
transcriptsUTR3 <- mapply(function(UTR, CDS, strand)
{
if(strand == '+') UTR[UTR > CDS[length(CDS)]] else UTR[UTR < CDS[1]]
}, transcriptsUTR, firstCDS, as.list(strands), SIMPLIFY = FALSE)
另
That shouldn't be too difficult to figure, given you have UTRs annotated.
5'-UTRs are those UTRs at the 5' end of a transcript
3'-UTRS are those at the 3' end of a transcript
