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3.0 years ago
Francesco ▴ 20
Whenever I try to add a reference fasta file for computing the GC content in the GetBamCounts function:
my.countsV6 <- getBamCounts(bed.frame =AgilentV6, bam.files = BAMFiles, include.chr = TRUE, referenceFasta = "data/hg19.fa" )
I get an error like this:
Reference fasta file provided so ExomeDepth will compute the GC content in each window Error in value[[3L]](cond) : record 38397 (chr11:134201957-134202041) failed file: data/hg19.fa
Everything works fine without the referenceFasta. I tried both with the UCSC and Ensembl build but I get the same error on a different chromosome.
R version 3.6.3 (2020-02-29) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363) Matrix products: default locale:  LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252  LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages:  parallel stats4 stats graphics grDevices utils datasets methods base other attached packages:  GenomicRanges_1.38.0 GenomeInfoDb_1.22.1 IRanges_2.20.2 S4Vectors_0.24.4 BiocGenerics_0.32.0  ExomeDepth_1.1.15 readr_1.3.1
I just got the same error as your. Could you clarify after calculated GC content?
How did you manually add GC contents column to your dataframe?
Thanks in advance