I have a problem using ExomeDepth with a referenceFASTA file. I analysed app. 500 target genes (>7000 Exons, hg19) and without including a FASTA file and the GC content everything worked fine.
As GC content influencing amplification, coverage and CNV detection, I want to include this factor. Therefore I tried several things to get appropiate FASTA sequences.
mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") FASTA <- getSequence(chromosom,start,stop,type="hgnc_symbol",seqType="gene_exon", mart = mart)
`Reference fasta file provided so exomeDepth will compute the GC content in each window Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘scanFa’ for signature ‘"data.frame", "GRanges"’`
A DNAStringSet instance of length 10 width seq  845 GTTGAAAAGTGATCAGGTTCATTTTATTGACTACACAGAAGCAATTCCATTT...GAGGAGGCAGATCACGGCGAAGACAATGAAGCTGTACGGGCCGAGGCCCTC  129 CCTGGATGAACGGGAAGATCAAGCCCACGGTGAAGTTGGAGAGCCAGTGCAC...GCCGAGAGGACTGCAGGAAGATCTCAGTGATGAGCAGCGCGGGTATGGGAC  77 CTGGGCCCGAGGGCATGTCCTATGACGTAGGAGATGACACAGACGATGCTGATGTATGGCATCCAGGACACTGTGTC  103 CCTGCAGTGCCAGAGCTGCAGTGAGCACGCAGCAGGCTATGAGGCAGATGGAGAAGCCCAGCAGCAGCAGCAGCCTCCGACCCAGGAGCTCCACCACGAACAC  112 CGGCGCAGAAGGTCATGACCACGTTCACGGCCCCGGTGCCGGCCGTCACGTA...CTCCTCCGGCACGCCGGCGCTCAGGTAGATCTGGTCCGCGTAGTAGTAGAT
Reference fasta file provided so exomeDepth will compute the GC content in each window Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘scanFa’ for signature ‘"DNAStringSet", "GRanges"’
3. Downloading human_g1k_v37.fasta.gz
Chromsome, Start & Stop including only the 7000 exon locations. With method 1 and 2, I was able to get target sequences, but the counting (getbamcounts) didn't work, different errors occur, warning something is wrong with the FASTA file. I think there are some file formatting issues.
my.counts<- getBamCount(data.frame(Chromsome, Start,Stop),
bam.files = bam.files,
include.chr = F ,
I dindn't tried the human_g1k_v37.fasta.gz so far, because I don't know how to load it in R.
Do you have an idea how to transform the files that they work or how to load the whole genome FASTA File?