User: poojitha.ojamies

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Posts by poojitha.ojamies

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Answer: A: Error while running SomaticSignatures
... Fixed! I used BSgenome.Hsapiens.UCSC.hg19 insead and it works :) Thanks for the pointer!   ...
written 3.1 years ago by poojitha.ojamies0
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Answer: A: Error while running SomaticSignatures
... Ah, you are right! They are two different builds. Should I use my own FA reference files or is there a better fix for this? > seqlevelsStyle(vr_new) [1] "UCSC" > seqlevelsStyle(BSgenome.Hsapiens.1000genomes.hs37d5) [1] "NCBI"    "Ensembl" ...
written 3.1 years ago by poojitha.ojamies0
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Error while running SomaticSignatures
... Hi, I am trying to run soamtic signature on a test data and enountered the following issue. Can someone explain what this problem is and how to fix it? Thanks!   > sca_motifs = mutationContext(vr_new, BSgenome.Hsapiens.1000genomes.hs37d5) Error in .getOneSeqFromBSgenomeMultipleSequences(x, nam ...
somaticsignatures written 3.1 years ago by poojitha.ojamies0 • updated 3.1 years ago by Andy Lynch100
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Input files for somaticSignature
... Hello, We use Varscan to make our somatic mutation calls. I would like to know if I can use the vcf files generated by Varscan for SomaticSignatures or i would need to redo the variant annotation with the variantannotator? Can I extract the relevant info from Varscan output instead?     ...
somaticsignatures written 3.1 years ago by poojitha.ojamies0 • updated 3.1 years ago by Julian Gehring1.3k

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