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Question: Chrom len file bedgraph to bigwig
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gravatar for djevo1
2.1 years ago by
djevo1 • 60
djevo1 • 60 wrote:

What is the best tool to use or where can .len files be found for the bedgraph to bigwig tool. I am specifically looking for len files for ensemble genome builds for humans.
.len prep data genome index • 985 views
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modified 2.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.1 years ago by djevo1 • 60
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gravatar for y.hoogstrate
2.1 years ago by
y.hoogstrate • 460
Netherlands
y.hoogstrate • 460 wrote:

Hello Djevo1,

Galaxy makes use of the following script: https://github.com/galaxyproject/galaxy/blob/dev/cron/build_chrom_db.py

The usage is explained over here: https://wiki.galaxyproject.org/VisualizationSetup#Get-genome-chromosome-length-files

Good luck,

Youri
ADD COMMENT • link modified 2.1 years ago • written 2.1 years ago by y.hoogstrate • 460

I saw this before, however we are using the ensemble build. In this case will using that script do the same thing or is there another method to generate the files.

ADD REPLY • link written 2.0 years ago by djevo1 • 60
1

Maybe https://toolshed.g2.bx.psu.edu/view/devteam/fasta_compute_length/de2db1bdfbf8 ? Or via the command line: https://www.biostars.org/p/118954/ ?

ADD REPLY • link written 2.0 years ago by y.hoogstrate • 460
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