User: Marco Blanchette

Reputation:
210
Status:
Trusted
Location:
United States/Kansas City/Stowers Institute for Medical Research
Last seen:
3 years ago
Joined:
5 years, 3 months ago
Email:
m**@stowers.org

Posts by Marco Blanchette

<prev • 20 results • page 1 of 2 • next >
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Answer: A: Is Bioconductor 3.0 compatible with R 3.1.2?
... Finding that on my Mac running R 3.1.1, BioConductor installs version 2.14 only, take a look:  > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.14 (BiocInstaller 1.14.3), ?biocLite for help A newer version of Bioconductor is available for this version of R,   ?BiocUpgrade ...
written 3.0 years ago by Marco Blanchette210
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Weirdness with the human org.Hs.eg.db annotation database
... I fumble on some oddities while using the org.Hs.eg.db. Unless I am missing something in how to work the the AnnotationDbi package, it seems that the Hs database as faulty entries in it.   There seems to be a one to many relationships between transcripts and genes. I.e. That individual transcri ...
homo sapiens annotationdbi written 3.1 years ago by Marco Blanchette210 • updated 3.1 years ago by Marc Carlson7.2k
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Comment: C: Best practices to find intersection among variants
... Thanks Michael, Just as a clarification, one needs to first re-cast the VCF as VRanges, right? I just tried it, only work if: intersectVCF <- function(v1,v2){ ## In the real life, I would make that a one operation but for the sake of clarity m <- as(v1,'VRanges?) %in% (v2,'VRanges ...
written 3.2 years ago by Marco Blanchette210
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Comment: C: Best practices to find intersection among variants
... All right! Thank you guys. Here is my little pipeline 1) slurping in the vcf files in a directory 2) Filtering out the one that didn?t passed the GATK filtering step (This could be probably be done during reading from file, couldn?t figure out how yet?) 3) finding the common one among all the files ...
written 3.2 years ago by Marco Blanchette210
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Comment: C: Best practices to find intersection among variants
... Thanks a lot, make sense. So, just to confirm, o.l <- findOverlaps(vcf1,vcf2) Where vcf1 and vcf2 are VCF object would not work, it would operate on the Granges and would consider the alt. -- Marco Blanchette, Ph.D. Genomic Scientist Stowers Institute for Medical Research 1000 East 50th Stree ...
written 3.2 years ago by Marco Blanchette210
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Best practices to find intersection among variants
... I am very very new to working with variants, maybe this question is very basic but I need to get kickstarted a bit? Just ran an analysis to find the common variation in a set of lab strains used in house in the haploid genomes of S. pombe. I used GATK best practices and I am at the stage where I ha ...
variantannotation genomes written 3.2 years ago by Marco Blanchette210 • updated 3.2 years ago by Julian Gehring1.3k
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problem reading bigwig files with rtracklayer from Ensembl mitochondrion chromosome name
... I just stumbled upon some oddities with rtracklayer and data generated from the NCBI/Ensembl annotation of the Drosophila genome. It seems like bigwig saved with the official NCBI/Ensembl/flybase mitochorion chromosome name dmel_mitochondrion_genome breaks the importation of a previously saved files ...
coverage annotation rtracklayer written 3.4 years ago by Marco Blanchette210
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using a connection with makeTranscriptDbFromGFF()
... Dear all, not sure if this is feasible but one would think it should I'd like to automate the creation of making transcript database from gff3/gtf files taken from ftp server without having to download the annotation. Some of the files (most likely all of them) would be compressed and would require ...
written 4.1 years ago by Marco Blanchette210
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Comment: C: bug in GenomicRanges gaps?
... though... sorry about the genes.noStrand... was working on a different example before posting... bad pasting... And yes, I was trying to find the gaps between genic regions regardless of there strand. I was doing the same operations as yours until I fumble onto gaps() which seemed to encapsulate ni ...
written 4.2 years ago by Marco Blanchette210
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Answer: A: bug in GenomicRanges gaps?
... Little bit more investigating let me realize that it happen when the seqinfo has seqLengths populated, check this out > genes <- GRanges(seqnames=c(rep("2L",3),rep("3L",3)), + ranges=IRanges(start=rep(c(20,200,350),2),end=rep(c(80,275,450),2))) ### Adding some chromosome width > seqlength ...
written 4.2 years ago by Marco Blanchette210

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