User: creasyt

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creasyt0
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Posts by creasyt

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Comment: C: Can't install rtracklayer - make: *** [ucsc/os.o] Error 1
... Good eye! Definitely an anaconda problem. I resolved it by symlinking to the correct version of regex.h.  Thanks for spotting the problem. ...
written 17 days ago by creasyt0
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Can't install rtracklayer - make: *** [ucsc/os.o] Error 1
... Hi, I'm unable to install rtracklayer because of some error regarding ucsc/os.o. I've attached a snippet of the installation routine with the error reported at the bottom. I've tried to install earlier version including the newest (1.40.2) but all give me the same error. I'm installing on CentOS 7 ...
rtracklayer written 18 days ago by creasyt0
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Can't install edgeR because of compilation error: make: *** [R_add_prior_count.o] Error 1
... Hi, I can't seem to install edgeR due to an odd compilation error (see below). The error appears to be something about "make: *** [R_add_prior_count.o] Error 1: Has anyone encountered this error? Any ideas what might be missing (lib dependency)? Thanks, -todd   > biocLite("edgeR") BioC_mir ...
edger compilation error written 6 months ago by creasyt0 • updated 6 months ago by Gordon Smyth33k
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Comment: C: Translation Error in predictCoding() for VariantAnnotation
... Hi Herve, I saw that, too. However, these are not start codons which is why I brought it up. Plus, I think that setting GENETIC_CODE is only to translate the nucleotide sequence. I *think* the codons are translated in another function later on in a separate function. I noticed that the only time sa ...
written 9 months ago by creasyt0
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Comment: C: Translation Error in predictCoding() for VariantAnnotation
... Sorry, the "**TTG**" was a mistake. I removed them from the post. I've added some code that I used to generate the custom txdb object which is for a RSV virus, the gff3 data, the fasta sequence, and the sessionInfo(). Let me know what else you need. ...
written 9 months ago by creasyt0
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Translation Error in predictCoding() for VariantAnnotation
... Hi, I'm noticing what appears to be an incorrect translation of a codon with predictCoding(). It's somewhat difficult to see but below is output of all nonsynonymous amino acid changes. However, variant 3 at bp 1002 shows an M for TTG rather than an L. Is this a bug? Clearly TTG is an L in the stan ...
variantannotation written 9 months ago by creasyt0 • updated 9 months ago by Hervé Pagès ♦♦ 13k

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