Inge Seim sciseim
sciseim
/ gist:69cbdb4060f2b3e19b08
Last active
August 29, 2015 14:10
— forked from jwaageSnippets/gist:5133941
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| library("rtracklayer") | |
| session <- browserSession("UCSC") | |
| genome(session)<-"mm9" | |
| query <- ucscTableQuery(session, "refGene") | |
| tableName(query) <- "refGene" | |
| getTable(query) -> refseq | |
| refseq[,c(2,3,4,5,6,7,8,13)] -> refseq | |
| refseq$"width" <- refseq$"txEnd"-refseq$"txStart" | |
| as.character(refseq[,1]) -> refseq[,1] |
sciseim
/ human-bodymap2.0-fpkms.bash
Created
February 3, 2014 04:16
— forked from ericminikel/human-bodymap2.0-fpkms.bash
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| # Eric Minikel | |
| # CureFFI.org | |
| # 2013-07-04 | |
| # Bash script to generate FPKMs from Ensembl Human Bodymap 2.0 RNA-seq data | |
| # Announcement of Human BodyMap 2.0 data availability: http://www.ensembl.info/blog/2011/05/24/human-bodymap-2-0-data-from-illumina/ | |
| # BAM list: ftp://ftp.ensembl.org/pub/release-70/bam/homo_sapiens/genebuild/ | |
| # STEP 1: DOWNLOAD THE BAMS FROM ENSEMBL |