Question

GenomeBrowse stream network data

1

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9.7 years ago

calizarr ▴ 10

So I am trying to figure out a way to get Golden Helix GenomeBrowse to accept my files from an ftp url. However, it won't detect them when I give it the address. Is there something specific I need to do?

helix golden network data genomebrowse stream • 1.8k views

ADD COMMENT • link updated 3.7 years ago by Ram 44k • written 9.7 years ago by calizarr ▴ 10

Ram · Answer 1 · 2015-04-17

1

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9.7 years ago

Gabe Rudy ▴ 320

From the GenomeBrowse main window, go to Add then click on the Url button on the left-hand side.

You put in the base directory in the top line, and hit Enter. It will then list all available sources at that location.

For example if you wanted to add:

ftp://ftp-trace.ncbi.nih.gov:21/1000genomes/ftp/data/HG00096/exome_alignment/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam

You would set the base path of ftp://ftp-trace.ncbi.nih.gov:21/1000genomes/ftp/data/HG00096/exome_alignment/ and then select the exome BAM file such as below:

ADD COMMENT • link updated 3.7 years ago by Ram 44k • written 9.7 years ago by Gabe Rudy ▴ 320

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Ah, so I noticed that you added the :21 to the ftp. I was missing that for my internal ftp and now it is in fact showing the BAM file. Though I get an "Unrecognized % expansion. Possibly the project was created with a different set of saved folders Plot has no data source." error.

However, does GenomeBrowse not accept vcf files via streaming ftp either?

ADD REPLY • link updated 3.7 years ago by Ram 44k • written 9.7 years ago by calizarr ▴ 10