User: poisonAlien
poisonAlien • 2.4k
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Cancer genomics
Posts by poisonAlien
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... Hi,
Whether a gene is a driver or not is usually done on large cohorts based on how frequently the gene is mutated. There are algorithms to identify such genes. How many cell lines do you have in your file ?
In case if you're only interested in a particular mutation,
- you will have to look at ...
written 4 days ago by
poisonAlien • 2.4k
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... They are Ensemble Gene IDs. See [here][1] for converting them to Gene symbols.
[1]: http://www.ensembl.org/Help/Faq?id=125 ...
written 24 days ago by
poisonAlien • 2.4k
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... > The "MAF" in vcf2maf refers to "Mutation Annotation Format", which was
> something unncessarily invented and confusingly named for cancer
> genetics.
So true! This also conflicts with [Multiple Alignment Format][1]
[1]: https://cgwb.nci.nih.gov/FAQ/FAQformat.html#format5 ...
written 7 weeks ago by
poisonAlien • 2.4k
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... Try [lncRNA-screen][1]
[1]: https://github.com/NYU-BFX/lncRNA-screen ...
written 8 weeks ago by
poisonAlien • 2.4k
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... We are seeking a bright, energetic individual with superior bioinformatic skills who can interact with approximately 10-15 post-docs/Ph.D. students; each of them are doing massively parallel sequencing of various tumors, RNA-Seq, ChIP-Seq, RNA array as well as combing the bioinformatics literature f ...
written 8 weeks ago by
poisonAlien • 2.4k
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... I believe that the papers that you're mentioning are looking at population based cnv's rather than sample wise. TCGA uses gistic to identify recurrent CN aberration in a cohort, which are potentially driver events.
Above file is a CBS output and not all entries are copy number alterations. Last co ...
written 11 weeks ago by
poisonAlien • 2.4k
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... how did you look at TCGA cnv data? Was it from GISTIC output ? ...
written 11 weeks ago by
poisonAlien • 2.4k
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Comment:
C: ABSOLUTE MAF error
... oh ! Okay, I think Absolute uses pre-computed purity and ploidy models from known cancer cohorts. I guess this is an issue if you're using non-human genome. ...
written 11 weeks ago by
poisonAlien • 2.4k
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... TCGA doesn't provide germline variants for privacy reasons. I think you will have to download BAM files and look by yourself. ...
written 12 weeks ago by
poisonAlien • 2.4k
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Comment:
C: ABSOLUTE MAF error
... Absolute requires column containing vaf, `t_vaf`. Maybe try adding it ?
maf$t_vaf = as.numeric(as.character(maf$t_alt_count)) / as.numeric(as.character(maf$t_depth))
edit:
also make sure chromosome names in MAF matches to that in segmentatioin file. Better remove `chr` prefix from both files. ...
written 12 weeks ago by
poisonAlien • 2.4k
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