Skip to main content

Tutorial Bedtools Bedtool


#!/bin/sh

##### PARAMTER for INTERSECT######:
## mention strandness
# -s
# print A , with number of Hit
#  -c
# print A , with number of bp overlap
# -wo



##### EXAMPLE ####
f1="coding.withrpt.bed.tmp"
f2="noncoding.withrpt.bed.tmp"
f1Out="coding.withrpt.bed"
f2Out="noncoding.withrpt.bed"

fCDS="refseqcoding.CDS.bed"

# bedtools intersect -s -c  -a $f1 -b $fCDS  > $f1Out
# bedtools intersect -s -wo  -a $f1 -b $fCDS  > $f1Out.bp

# bedtools intersect -s -c  -a $f2 -b $fCDS  > $f2Out
# bedtools intersect -s -wo  -a $f2 -b $fCDS  > $f2Out.bp

# bedtools intersect -s -wo -a test1.bed -b test2.bed



##### PARAMTER for GETFASTA ######:
## mention strandness
# -s
## input and output file
# -fi  -fo

##### EXAMPLE ####
fAllgeneBed="allGene.bed"
fAllgeneFasta="allGene.fasta"
# bedtools getfasta  -s  -fi /home/data/genomes/hg19/hg19.fa -bed $fAllgeneBed -fo $fAllgeneFasta

Comments

Post a Comment

Popular posts from this blog

MATLAB cross validation

// use built-in function samplesize = size( matrix , 1); c = cvpartition(samplesize,  'kfold' , k); % return the indexes on each fold ///// output in matlab console K-fold cross validation partition              N: 10    NumTestSets: 4      TrainSize: 8  7  7  8       TestSize: 2  3  3  2 ////////////////////// for i=1 : k    trainIdxs = find(training(c,i) ); %training(c,i);  // 1 means in train , 0 means in test    testInxs  = find(test(c,i)       ); % test(c,i);       // 1 means in test , 0 means in train    trainMatrix = matrix (  matrix(trainIdxs ), : );    testMatrix  = matrix (  matrix(testIdxs  ), : ); end //// now calculate performance %%  calculate performance of a partition     selectedKfoldSen=[];selectedKfoldSpe=[];selectedKfoldAcc=[];     indexSen=1;indexSpe=1;indexAcc=1;     if ( kfold == (P+N) )% leave one out         sensitivity = sum(cvtp) /( sum(cvtp) + sum(cvfn) )         specificity = sum(cvtn) /( sum(cvfp) + sum(cvtn) )         acc
5 comments
Read more

R tutorial

Install R in linux ============ In CRAN home page, the latest version is not available. So, in fedora, Open the terminal yum list R  --> To check the latest available version of r yum install R --> install R version yum update R --> update current version to latest one 0 find help ============ ?exact topic name (  i.e.   ?mean ) 0.0 INSTALL 3rd party package  ==================== install.packages('mvtnorm' , dependencies = TRUE , lib='/home/alamt/myRlibrary/')   #  install new package BED file parsing (Always use read.delim it is the best) library(MASS) #library(ggplot2) dirRoot="D:/research/F5shortRNA/TestRIKEN/Rscripts/" dirData="D:/research/F5shortRNA/TestRIKEN/" setwd(dirRoot) getwd() myBed="test.bed" fnmBed=paste(dirData, myBed, sep="") # ccdsHh19.bed   tmp.bed ## Read bed use read.delim - it is the  best mybed=read.delim(fnmBed, header = FALSE, sep = "\t", quote = &q
Post a Comment
Read more