Question: Chrom len file bedgraph to bigwig
0
gravatar for djevo1
19 months ago by
djevo160
djevo160 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 • 790 views
ADD COMMENTlink modified 19 months ago by Jennifer Hillman Jackson25k • written 19 months ago by djevo160
1
gravatar for y.hoogstrate
19 months ago by
y.hoogstrate460
Netherlands
y.hoogstrate460 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 COMMENTlink modified 19 months ago • written 19 months ago by y.hoogstrate460

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 REPLYlink written 19 months ago by djevo160
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 REPLYlink written 19 months ago by y.hoogstrate460
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