Hi everyone,
I am working on a project about copy number variant calling algorithms. One question I am asking is that if GC content correlated with the success rate of CNV calling, and to answer that I would need the actual sequence. However, I don't have the original bam or bed files; I only get the output file from the different CNV calling algorithms, and a corrected consensus file among all of these algorithms. (It would be hard for me to explain how did I calculate consensus, so I would leave that part out for now.)
The information I have now is basically just chromosome and position on the chromosome.
"example: ch1:1453:20918"
I am thinking about use these positions info to line back to hg19 reference data, and get the exact sequence, then calculate the GC content by hand.
I called the getSequence function in biomaRt package, the call returned a dataframe with two columns: sequence and gene symbol. When I choose seqType="cdna", I was expecting the sum of length of each fragment/gene equal to the length of the calling segment(end-start), but it did not.
ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
result = getSequence(chromosome=1, start=28028201, end=32976095,type="entrezgene",seqType="cdna", mart=ensembl)
#count all the nucleotides
count <- 0
for (i in 1: nrow(result)){
length <- length(unlist(strsplit(result[i,1], split = "")))
count <- count+length
}
end-start
[1] 4947894
count
[1] 16861601
Here is the detailed info about categories in seqType: The type of sequence returned can be specified by the seqType argument which takes the following values:
'cdna': for nucleotide sequences
'peptide': for protein sequences
'3utr': for 3' UTR sequences
'5utr': for 5' UTR sequences
'gene_exon': for exon sequences only
'transcript_exon_intron': gives the full unspliced transcript, that is exons + introns
'gene_exon_intron' gives the exons + introns of a gene;'coding' gives the coding sequence only
'coding_transcript_flank': gives the flanking region of the transcript including the UTRs, this must be accompanied with a given value for the upstream or downstream attribute
'coding_gene_flank': gives the flanking region of the gene including the UTRs, this must be accompanied with a given value for the upstream or downstream attribute
'transcript_flank': gives the flanking region of the transcript exculding the UTRs, this must be accompanied with a given value for the upstream or downstream attribute
'gene_flank': gives the flanking region of the gene excluding the UTRs, this must be accompanied with a given value for the upstream or downstream attribute
Am I understanding the concept or output wrong? Or should I change some parameters to make this work?
Appreciate all your help in advance.
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