convert tdf to bigwig...

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Nick Schurch

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Dec 12, 2014, 5:46:56 AM12/12/14
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Hi All,

What's the right way to do this? 

Incidentally, why does IGV still bother with tdf files since they aren't widely read?

Nick

Jim Robinson

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Dec 12, 2014, 8:57:15 AM12/12/14
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NIck,

I assume you don't have the original source files and that's why you are asking, is that correct?

IGV still "bothers" because a lot of people have a lot of TDF files.   It was developed by yours truly before there was a bigwig.    Bigwig is supported as well,  so you don't have to use them.  TDF does do some things bigwig doesn't,  e.g. it supports multi-column data file formats.


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Nick Schurch

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Dec 15, 2014, 4:59:51 AM12/15/14
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Hi Jim,

Its public data I'm looking at. I have the sra files so in principle I could convert these to fastq and realign them, but 1) that not exactly the same as the data used in the publication and 2) they provide their processed data at tdf files. I get supporting a legacy format, but this is recent data so I have no idea why the default file for outputting tracks like this wouldn't be a more widely supported format.

Anyway, all I really need is to be able to convert them. So, how exactly do I do that?

Nick

Jim Robinson

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Dec 15, 2014, 9:08:55 AM12/15/14
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There is an (undocumented) option in igvtools to convert tdf files to
"bedgraph", you should then be able to convert that to bigwig.

igvtools tdftobedgraph input.tdf output.bedgraph

Tyler Miller

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Apr 30, 2015, 2:07:42 PM4/30/15
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Hi Jim,
Thanks for the response and work-around. I would also like to do this, but when I am in IGV and Tools>Run igvtools...  the "Command" drop down menu does not have this option and will not allow me to input it manually. Am I missing something? How do I run this undocumented command?
Thanks!
Tyler

Jim Robinson

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Apr 30, 2015, 2:11:36 PM4/30/15
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Hi Tyler,

You need to run igvtools from the command line, this is not available in the UI.

Jim

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