Questions & Answers

[Mike Sqcrft]

Question 1: I don't understand the difference between IP_BAM = ip and INPUT_BAM = input
from TopHat i have only GTF file and input BAM files, what are the ip BAM files ?

Answer: IP_BAM: specifies a number of IP samples from the untreated condition in bam format

INPUT_BAM: specifies a number of Input control samples from the untreated condition in bam format

The input sample is a kind of control sample obtained from all the fragmented RNA without the immunoprecipretation step. Please install the latest version, and check the help of ‘exomepeak’ function with: ?exomepeak

With the latest version, gene annotation may be downloaded from internet directly from UCSC, with:

result = exomepeak(GENOME="hg19", IP_BAM=IP_BAM, INPUT_BAM=INPUT_BAM)