Cisgenome Browser With Bar Files Vs Igv With Wig Files

Question

[Hamilton]

I am looking at the interesting peaks on cisgenome browser with bar files(i generated them from bam file using converting functions in cisgnome such as barTobed).

The other one, I uploaded wig files generated from MACS on IGV viewer.

They are coming from the identical sample and i am comparing on both browsers.

Btw. although the peak regions are exactly matched between two browsers. but IGV looks more fancy and reliable peaks, whereas the peaks on cisgenome browser uploaded with bar files are also shown in the same regions. but the shape of peaks looks rough and crude. so. it looks like random peaks. I expected exactly same shapes for peaks on both. but not like that.

So, one thing i doubt is that, i wonder if there are any pre-processing or normalization steps prior to bar files using bam files?

And one more question for IGV viewer, unlike other browsers such as UCSC or cisgnome, it provides only one strand information and there are no conservation maps. is there any way for me to add them on IGV?

Any comments or suggestions??

[Hamilton]

let me try to make it clear. -- the main question was whether i need any preprocessing procedures in conversion step from bam files to bar files for cisgenome or not. This is chipseq data of TF.

Answer 1

[Ying W]

IGV by default will not display reads marked as duplicates, you will need to be more specific when talking about the different file types, im guessing everything came from bam files and when you say bar and barToBed it is just a typo of bam. If you search around you will see a lot of posts about preprocessing chip-seq (since you are taling about cisgenome i assume you have chipseq data) data. One of the common steps is duplicate marking. I am not quite sure how you would do normalization

For conservation, you will need one of the phastCons files here: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ (assuming you are working w/human hg19) http://genomewiki.ucsc.edu/index.php/Conservation_Track gives some more information of the different tracks