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vplagnol / ExomeDepth

ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
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For using it on Rstudio windows #12

Open amrita1983 opened 6 years ago

amrita1983 commented 6 years ago

Hi,

Can i use the package in Rstudio of windows? My R version for R studio is 3.4

amrita1983 commented 6 years ago

Hi, I have installed in in my Rstudio, but when I ma giving this command error is coming my.counts <- getBamCounts(bed.frame = exons.hg19,bam.files = Lib1.bam,include.chr = FALSE,referenceFasta = hg19) Error in getBamCounts(bed.frame = exons.hg19, bam.files = Lib1.bam, include.chr = FALSE, : object 'hg19' not found I kept all the files in the data folder of exomedepth where should i keep them? how can I load my own bed file. need help.

evolvedmicrobe commented 6 years ago

For referenceFasta = hg19 there is no variable called hg19 so you are receiving the error. You need to specify a path to the file as a string in quotes, e.g. referenceFasta='/some/where/hg19.fasta'

amrita1983 commented 6 years ago

Thank you for the reply, but even though I am changing the path it is not taking it. Also it is showing error for all the other files. All the files i kept inside the data folder of Exomedepth folder in R. Need help to parse the files.

laranonell commented 6 years ago

Upps, i did not realize that the issue was closed, I opened a new issue... Dear Vincent,

I am facing I guess a similar problem

bis1 <- getBamCounts(bed.frame = regions.df, bam.files = file.path("./BAMs_all","qG16018101bis.final.bam"), include.chr = FALSE, referenceFasta = "Z:/RNA_seq/Ref_Genomes_fa/hg19.fa") Reference fasta file provided so ExomeDepth will compute the GC content in each window Error in value[3L] : record 1 (1:1138878-1139350) failed file: Z:/RNA_seq/Ref_Genomes_fa/hg19.fa

I have tried also with hg38.fa (both fasta files are being used by other methods with no problems. If I ommit the fasta files it works but results are not what I expect so I am trying to make the method adjust by GC content as a first trial. Best,

Lara