Conversion from tdf to bed format

Question

[anwesha.ghosh.btech]

I am trying to use ChIP-Seq data from GEO that has been posted in tdf format. I want to convert it to tdf format with chromosome, start and stop coordinates as well as signal intensity. How do I do it? A previous post talked about converting it from tdf to bedgraph and from bedgraph to bed but the fourth column with the signal intensity was missing in the bed file.

Thanks! Anwesha Ghosh Postdoctoral Associate SBP Medical Discovery Institute

Answer 1

[Sukhi Singh]

The question is not bit clear, "posted in tdf and want to re-convert to tdf?" I think you meant converting .tdf to .bed Firstly, Tdf (tile density format) is native to IGV for faster display and nvaigation. You could convert TDF to BED, by using igvtools

igvtools tdftobedgraph  file.tdf file.bedgraph

Depending on what you want to do further, a bedGraph can be converted to other formats.

Lastly, why does a BED file doesn't have an intensity but a BedGraph file has, because BedGraph is an average file obtained from BED. A BED file can have a scrore which is different from the intesity you are talking about.

Read more : BedGraph Format and BED Format

[spz1st]

Can you tell me where is the document about tdftobedgraph? I just installed igvtools but tdftobedgraph is not listed as one of the commands when I tried igvtools help. Thanks.

[O.rka]

Any chance you know how to get the headers on this?