trouble with predictCoding( function

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vakul.mohanty ▴ 20

@vakulmohanty-8232

Last seen 7.4 years ago

United States

I'm attempting to annotate SNPs from VCF files I have downloaded from the TCGA dataportal. I'm able to identify their locations, but when i try to use the predictCoding() "coding <- predictCoding(vcf,txdb,seqSource = Hsapiens)" to identify effect of the variants in the coding regions I get the following error

Error in .getOneSeqFromBSgenomeMultipleSequences(x, names[i], start[i], :
sequence ^1$ not found

Could someone suggest a work around or a way to fix the error.

the version of R i use is version.string R version 3.2.0 (2015-04-16), in case that makes a difference.

Thank you,

> version

snp variantannotation predict coding • 1.4k views

ADD COMMENT • link 9.4 years ago vakul.mohanty ▴ 20

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Hi,

Please show your sessionInfo(). What are txdb and Hsapiens? How did you get them? I suspect the problem is that the objects you supply to the vcf, txdb, and seqSource arguments don't use the same chromosome naming conventions.

H.

ADD REPLY • link 9.4 years ago Hervé Pagès 16k

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