JOBS mESC Library
Q: How can I perform motif analysis for all ChIP peaks ?
A: As default, ChIP-Array 2 performs motif analysis for peaks only in promoter region of target genes. To perform motif analysis for all peaks, you have to download the job and get the peaks from peaks-<FACTOR>.txt. You can submit the peaks to http://meme.nbcr.net/meme/cgi-bin/meme-chip.cgi or do it with standalone version of MEME, HOMER and related tools.
Q: How can I get the target genes detected with the contribution of long-range interaction ?
A: You can intuitively browse the targets in JBrowse and check whether they have TFBS with [<REGION>] in name. Or you can download the job and examine the file peaks-<FACTOR>.txt, the genes with [<REGION>] in peak name are the targets detected with the contribution of long-range interaction. You can also use the simple bash code to do that: grep "\[chr" peaks-<FACTOR>.txt | cut -f7. [<REGION>] denotes the original peak coordinates.
Q: I have neither the ChIP-X nor transcriptome data, can I get the putative targets of a factor ?
A: Yes. You can choose to use our builtin data or putative TFBSs by PWM scanning.
Q: Where can I check the TFBSs in the distance around TSS I defined for the method "Rank Product" ?
A: You may download the job and check them in peaks10k-<FACTOR>.txt.
Q: How can I perform co-occupancy analysis for jobs in mESC library ?
A: You can click Make it my job in the mESC library page, and then will find the job in your job list. Check the job and other other job you want to combine with, click Co-occupancy Analysis in job list.
Q: How to view a particle location in JBrowse in the popup window ?
A: Click the Full-screen view on the top-right corner, and input the region in the region input box.

Q: Why I cannot find all the peaks that I uploaded ?
A: JBrowse will only show the peaks in the targets` promoter regions. If you want to check all the peaks, please download the job and check chip-x.bed file.
Q: How can I access my jobs in other browsers ?
A: Just copy the job URL and paster it to other browsers, the job will be automatically added in to you job list in other browsers.
Login Register