User: Scott McKay

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Scott McKay20
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Posts by Scott McKay

<prev • 19 results • page 1 of 2 • next >
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(Closed) Indexing Genome Commands in Linux (hummingbird-ucsc)
... Hey all, I am having trouble indexing my reference genome (mm10) with bowtie 2. It keeps stalling / lagging after it starts indexing. As in it begins, but then gets stuck in a loop soon after and cannot finish. Anyone else run into this problem? Or know another way to go through indexing a genome f ...
bowtie2 chip-seq linux written 5 months ago by Scott McKay20 • updated 4 months ago by Biostar ♦♦ 20
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biomaRt Biotype Predictions
... How accurate is biomaRt's biotype prediction? I just ran a gene list through it (using ENSEMBL ID) and got a list of 'miRNAs' but GeneCards is telling me that some of them are coding genes??? Not sure what is going on, can anyone shed some light? ...
R biomart biotype written 8 months ago by Scott McKay20 • updated 8 months ago by Emily_Ensembl21k
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Comment: C: Gene Locus to ENSEMBL ID
... I looked at `searchAttributes(mart=ensembl, pattern=locus)` and then searched the Attributes for some loci information but turned up nothing ...
written 9 months ago by Scott McKay20
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Gene Locus to ENSEMBL ID
... Is there some way (biomaRt or not) that will allow me to convert the gene locus (NM_###) to it's ensembl gene id? ...
R biomart written 9 months ago by Scott McKay20 • updated 7 months ago by Biostar ♦♦ 20
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Comment: C: Molecular Function from ENSEMBL ID
... Hey Kevin, Thanks man! Really appreciate your insight! ...
written 9 months ago by Scott McKay20
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Molecular Function from ENSEMBL ID
... Is there an attribute in biomaRt that will allow me to see the BASIC function of a gene given its ENEMBL ID? I have been searching for a while but 'description' is not desired and I cannot find a 'function' or 'molecular' attribute. I want to get the following: TGIF1......Transcription Factor XIST ...
R gene-function high-throughput written 9 months ago by Scott McKay20 • updated 9 months ago by Kevin Blighe61k
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Comment: C: Microarray Probe IDs to ENSEMBL ID
... Hi, Sorry for the late reply. The query was as follows: `library(biomaRt) ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") probeids=read.table(file.choose()) ##single column txt file of probe ids getBM(attributes=c('affy_hugene_1_0_st_v1', 'ensembl_gene_id'), filters = 'affy_hugen ...
written 9 months ago by Scott McKay20
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Comment: C: Microarray Probe IDs to ENSEMBL ID
... Hi Ben, biomaRt gave me each probe ID mapped to multiple ENSG# IDs. As in 1 probe had been assigned to multiple genes. I would understand if one gene ID had multiple array IDs, but that does not seem to be the case. Any insight on this? ...
written 9 months ago by Scott McKay20
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Microarray Probe IDs to ENSEMBL ID
... I am currently converting a list of microarray probe ids to ENSEMBL IDs through biomaRt. I am currently in excel and I am seeing the same probe ID mapped to two different ENSEMBL IDs. Any idea what this means? I thought ENSEMBL IDs were based on the genes, not splicing variates or isoforms. Thanks! ...
gene R ensembl microarray high-throughput written 9 months ago by Scott McKay20 • updated 9 months ago by Ben_Ensembl1.5k
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Does anyone have experience with the massiR package in R?
... Has anyone used the massiR package? I am having trouble extracting the Y Chr data. Can someone help me out? >library(massiR) >data(y.probes) >probes <- data.frame(y.probes["affy_hg_u133_plus_2"]) >dataset <- read.table(file.choose()) >massi.y.out <- massi_y(dataset, probes) ...
yprobes sex microarray massir written 9 months ago by Scott McKay20

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