Question: Genome Coverage without hg19 reference genome
gravatar for yungchihlai
2.7 years ago by
yungchihlai10 wrote:


I have human hg19 RNA-Seq bam files, and would like to use Genome Coverage to convert bam to BedGraph format (fig1). However, I cannot find the hg19 genome. Could you help me? Thanks a lot.




genome coverage bedtools • 936 views
ADD COMMENTlink modified 2.7 years ago by Jennifer Hillman Jackson25k • written 2.7 years ago by yungchihlai10
gravatar for Jennifer Hillman Jackson
2.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The input for the "genome" field is not another BAM file, but a file of coordinates such as those in interval, bed, gtf, etc. format. Appropriate formats will be detected and appear in the pull-down menu (as long as the "datatype" metadata is assigned).

The public Main Galaxy instances are down for scheduled maintenance today, so you can try this again later tonight or tomorrow. Please follow here for updates:

Thanks, Jen, Galaxy team


ADD COMMENTlink written 2.7 years ago by Jennifer Hillman Jackson25k

Hi Jennifer,

Thanks a lot. In fact, I would like to build a bigwig file from a RNA-Seq bam file. Previous, I use (1) Create a BedGraph of genome coverage, and (2) Wig/BedGraph-to-bigWig to do it. However, this time, I cannot find the function of “Create a BedGraph of genome coverage”.  I think that “Genome Coverage” could be the same with “Create a BedGraph of genome coverage”, but maybe I am wrong. Could you teach me how to convert an hg19 RNA-Seq bam file to a bigwig file for uploading to the UCSC Genome Browser? I really appreciate your help.

Best, Gary

ADD REPLYlink written 2.7 years ago by yungchihlai10

Ah, yes, this is the correct tool to use for the transformation. It is from the recently updated bedtools tool suite from the IUC. Prior tools are present but with updated names and new tools are available. 

Although, converting it is not strictly necessary with a BAM dataset of this size - changing the track settings at UCSC can give a compressed view (try "dense"). Also, bigWig data is not really loaded at UCSC, rather it is hosted from an outsider server (like Galaxy or any other FTP/HTTP URL) and portions of it are sent to UCSC on demand for visualization. You may know this - just clarifying for whoever else may read this.

The screen shot does show a problem - the reference genomes on the instance should be in the pull-down menu, not datasets from the history (as far as I know - the updated form is very new). The entire genome is used for the task this tool does, not specific regions/windows (that is different tool).

I'll bookmark this question and take a look when the server is back up and find out if there is a problem with the new suite or just this tool (server configuration, etc). It is possible that the screenshot was taken around the same time the server was going offline, and that caused some form trouble (odd, but possible), but we'll know for certain soon exactly what is going on.

Thanks for clarifying! Jen


ADD REPLYlink written 2.7 years ago by Jennifer Hillman Jackson25k

Hi Jen, Many thanks for your help. I found that there is no any reference genome after the server is back up (fig2). Could you help me? Thanks a lot.

fig2 enter image description here

ADD REPLYlink written 2.7 years ago by yungchihlai10
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