This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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] |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
sort -b -k18 inputfile.txt > outputfile.txt |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
GTF2TranscriptDB <- function(gtf.file, out.file = NULL, verbose = TRUE) | |
{ | |
require(rtracklayer) | |
require(GenomicRanges) | |
require(GenomicFeatures) | |
min.info <- c("gene_id", "transcript_id", "exon_number") | |
if (verbose) message("Importing ", gtf.file) | |
gtf <- import.gff(gtf.file, asRangedData = FALSE) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
read.delim("/Volumes/BP_NextGen/jwg/Projects/Porse/TET1/homologene.data", stringsAsFactors=F) -> homologene | |
split(homologene, f=homologene[,1]) -> hSplit | |
#Tax ID: Homo 9606 | |
#Mus: 10090 | |
getHumanAndMouseHomologues <- function(x) | |
{ | |
if (c(9606)%in%x[,2]&&c(10090)%in%x[,2]) | |
{ |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
plot + scale_fill_discrete(name="Experimental\nCondition", | |
breaks=c("ctrl", "trt1", "trt2"), | |
labels=c("Control", "Treatment 1", "Treatment 2")) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
library("rtracklayer") | |
session <- browserSession("UCSC") | |
genome(session)<-"mm9" | |
query <- ucscTableQuery(session, "refGene") | |
tableName(query) <- "refGene" | |
getTable(query) -> refseq |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# substitute cut -f 20 with column containing sequence. Sed bit removes last line | |
cat file_with_sequences.bed | cut -f 20 | awk '{print; if (FNR % 1 == 0 ) printf ">" NR "\n";}' | sed -n '$!p' > sequences.fasta |