Kent Utils Bigwig Question

[Evan]

Good afternoon,

I am attempting to generate bigwig files from our bam dataset aligned
with GRCH37, but need a chromosone length file. I found one for UCSC,
but is there one for the ensemble build, or better a tool to generate it.

Regards,
Evan Clark

[Hiram Clawson]

Good Morning Evan:

1. convert fasta assembly to 2bit file:
faToTwoBit assembly.fa.gz assembly.2bit
2. Extract chrom sizes from 2bit file:
twoBitInfo assembly.2bit stdout | sort -k2nr > assembly.chrom.sizes

Or use faSize command:
1. faSize -detailed assembly.fa.gz | sort -k2nr > assembly.chrom.sizes

--Hiram

[evan clark]

Good afternoon Hiram,

I am attempting to load bigwig tracks to view in the UCSC genome browser. I am using public links from our server but I need to set the mime type for the bigwig files. Should they simply be download or a stream to ucsc?

Regards,
    Evan Clark

Hiram Clawson

November 17, 2016 10:31 AM

Good Morning Evan:

1. convert fasta assembly to 2bit file:
   faToTwoBit assembly.fa.gz assembly.2bit
2. Extract chrom sizes from 2bit file:
   twoBitInfo assembly.2bit stdout | sort -k2nr > assembly.chrom.sizes

Or use faSize command:
1. faSize -detailed assembly.fa.gz | sort -k2nr > assembly.chrom.sizes

--Hiram

Evan

November 16, 2016 7:12 PM

[Brian Lee]

Dear Evan,

Thank you for using the UCSC Genome Browser and your question about using public links form your server to visualize bigWig files.

It seems unlikely that any mime type is involved, however, there is a necessity that bigWig files be placed on a server that offers byte-range requests. A quick way to test if your server location offers byte-range requests is to use the curl -I command. Here is an example when pointed to an example bigWig file.

curl -I http://genome.ucsc.edu/goldenPath/help/examples/bigWigExample.bw

...

Accept-Ranges: bytes

These byte-range requests are needed so that a request for only the data from the bigWig file that is currently being viewed in the Browser is sent over the internet. This has the advantage of not transferring large files (especially sizable bam files), but some system administrator restrict such constant byte-range requests, as it can increase traffic and allow people to host other streaming data, such as pirated videos.

If byte-range requests are not enabled at your location, you may want to contact your system administrators to allow this, as although the requests are frequent, only a small amount of information is sent over the interent. In case it is of help for your system administrators here is a section about connection issues that may be useful: http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines#Help_for_connection_issues

Another option to is to host your data at a free site such as the NSF funded CyVerse. See this previously answered question for some information about hosting your data at CyVerse and how to create "Send to Genome Browser" links that support byte-range requests: https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/_Ws2jxNfJV4/0c5aGb_PAQAJ

Here is also an example of using curl -I on a file at CyVerse to see how byte ranges are enabled there:

curl -I https://de.cyverse.org/anon-files/iplant/home/brianlee/bigBedExample.bb

...

Accept-Ranges: bytes

Thank you again for your inquiry and using the UCSC Genome Browser. Please let us know if you continue to have a problem after enabling byte-range requests. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data (such as a URL to your private data), you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UCSC Genomics Institute

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