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Tool: cnv_facets: somatic Copy Number Variant calling using the facets package

tool cancer somatic command line facets cnv written 9 weeks ago by dariober ♦ 9.9k

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250

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readSnpMatrix in FACETS gives error

facets purity cnv ploidy written 9 months ago by hshah • 20

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883

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Merging CNVs from multiple tumor samples from the same patient

multiple samples ngs facets cnv metastasis written 18 months ago by sey • 10 • updated 18 months ago by markus.riester • 290

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751

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Filter out Non-Diploid segments in FACETS data

R facets cnv sequencing written 21 months ago by sviatoslav.kendall • 480

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Recent Replies

C: Gene name and ensembl ids by ATpoint ♦ 13k
True: Only protein-coding: Min. 1st Qu. Median Mean 3rd Qu. Max. 1.000 2.00...
C: Gene name and ensembl ids by i.sudbery ♦ 3.7k
I think this would be even higher if you limited it the ~20,000 protein coding genes. Very few pr...
A: Change NBCI accession numbers to UNIPROT identifiers by b.nota ♦ 6.1k
You can use the uniprot website: https://www.uniprot.org/uploadlists/ Use as input "RefSeq Prot...
C: GMAP error - Problem Sequence: TRINITY_DN422143_c0_g1_i1 (301 bp) by dukecomeback • 40
I'm not so sure if it has something to do with the header of the fasta sequences. Keeping the hea...
C: Gene name and ensembl ids by ATpoint ♦ 13k
In fact, checking the latest GENCODE release for human, there are 58381 annotated genes. Of these...
A: augustus output - how is the incompatible hint groups determined? by dukecomeback • 40
I'm a little disappointed with Augustus, some times I know the hint is corrected, however no matt...
C: A list of human cell cycle genes for Seurat by Pestudkaru • 20
Thank you genomax but I've already seen both of those links and neither has the complete informa...
C: How to create a covariate file for MutSigCV using gene expression values from ot by sm.hashemin • 60
Having the same question here, did you find out where this value comes from?
C: Samtools: Question about filtering BAM file using flag by genomax ♦ 62k
See [SAM Format site][1] for explanation of the flags. [1]: https://www.samformat.info/sam-fo...
C: dNdScv error: Zero coding substitutions found in this dataset by F • 3.2k
Thank you very much to be this much patient and helpful. Actually I have my own independent data ...
C: Gene name and ensembl ids by genomax ♦ 62k
Not necessarily. There can be more than one transcript variants.
C: Gene name and ensembl ids by ATpoint ♦ 13k
Hi, please google `isoforms` and `alternative splicing`.

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