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:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicRanges_1.38.0 GenomeInfoDb_1.22.1 IRanges_2.20.2 S4Vectors_0.24.4 BiocGenerics_0.32.0
[6] ExomeDepth_1.1.15 readr_1.3.1
•
written
by
Francesco •
Solved! It's very likely it was an overflow problem that R encounters with files bigger than 2GBs (as the hg19 fasta file) I manually computed the GC content of all the exonic regions with bedtools:
$ bedtools nuc -fi hg19.fa -bed S07604514_hs_hg19/S07604514_Covered_edit.bed | awk '{$4=""; print $0}' > AgilentV6_exons_GC_count.txt
Than I manually added the GC contents column to the my.countsV6 dataframe
Hello
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
JK
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