Conversion of raw data into bedgraph files

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Leena Shah

Jun 16, 2023, 12:39:55 PM6/16/23
to Integrated Genome Browser Help Desk
Hello again,

Some of the peaks of this chromatin immunoprecipitation followed by sequencing (ChIP-seq) data when uploaded as bedgraph files appear aberrant, i.e., not as themselves but as almost rectangular boxes, the likely reason for it being that they are not original files. Accessed from the same link --> SRP216996 -->, could you please convert the four samples into bedgraph files?

Thank you,

Leena Shah

Nowlan Freese

Jun 21, 2023, 1:59:12 PM6/21/23
to Integrated Genome Browser Help Desk
Hi Leena,

The supplementary file data at the GEO link ( contains the following columns:

Chromosome   start   stop   score
GL456210.1 82700 86700 1.619387283

So the data just provide a region where peaks were called, which in IGB will show up as boxes/rectangles when viewed as bedgraph. 


Bedgraph is a good way to look at these data in IGB as you can see the differences in scores easily, but I've also attached the same data as a bed file. If you look at the bed file in IGB you may want to right-click on the track in IGB and select Color by... and then select Score.

The SRA data link ( is most likely raw data for the samples. The raw ChIP-Seq data would need to be aligned and peaks called in order to view the peak data. There are many great tutorials and videos on the web for aligning/calling peaks. I have an older video on YouTube that uses Galaxy:

Let me know if this helps!


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