Annotate bedfile with Transcript, Exon No & CDS

Question

[mrxcm3]

I have a BED file containing sequencing gaps

17  41223034    41223081
13  32929236    32929276
17  7574019 7574057

I would like to annotate this BED file with gene symbol, transcript id (RefSeq) and map the genomic coordinates to the CDS.

I have been trying to use GenomicFeatures in R to do this, and have got part way.

# import BED as GRanges object
bedfile <- rtracklayer::import.bed('./data/test.bed')

# import refseq transcripts as TxDB object
refseq_txdb <- makeTxDbFromUCSC(genome="hg19", tablename="ncbiRefSeq")

# split cds by transcript
cds  <- cdsBy(x = refseq_txdb, by = c("tx"), use.names=TRUE)

# map between genomic and cds coordinate system
bed2cds <- mapToTranscripts(x = bedfile, transcripts = cds, intronJunctions=TRUE)

This gives me a GRanges object that has the RefSeq IDs and CDS coordinates. However, I cannot easily find a way to update each entry of this object with Gene ID (Symbol) and Exon Number. And advice greatly appreciated.

GRanges object with 8 ranges and 3 metadata columns:
            seqnames      ranges strand |     xHits transcriptsHits  intronic
               <Rle>   <IRanges>  <Rle> | <integer>       <integer> <logical>
  [1]    NM_007298.3   1538-1584      - |         1           43630     FALSE
  [2]    NM_007294.4   4850-4896      - |         1           43631     FALSE
  [3]    NM_007297.4   4709-4755      - |         1           43632     FALSE
  [4]    NM_007299.4   1538-1584      - |         1           43633     FALSE
  [5]    NM_007300.4   4913-4959      - |         1           43634     FALSE
  [6]    NM_000059.3   7247-7286      + |         2           35159     FALSE
  [7] NM_001276697.2 -1986--1987      - |         3           43034     FALSE
  [8] NM_001126113.2   1042-1041      - |         3           43046      TRUE
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Answer 1

[Kevin Blighe]

If going this approach via rtracklayer, then you could do an additional overlap by following the code here: A: How to extract the list of genes from TCGA CNV data

Kevin