Question: Galaxy 101 Tutorial BED File Output
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gravatar for yvonne.turquoise
2.0 years ago by
yvonne.turquoise0 wrote:

To whom It May Concern,

I am a new user and have no prior bioinformatics knowledge.

I must be overlooking something small or basic but I cannot seem to identify the number of SNPs at a glance presented in the tutorial "Galaxy 101".  There seem to be a part (in the very beginning of the tutorial) that SNP data is gathered from the UCSC data base and presented in a BED file format as output. 

In section 2.0 after the joining tool has been used, it is stated that one must be able to see 48 SNPs. "Let's take a look at this dataset. The first six columns correspond to exons. The last six correspond to SNPs. You can see that exon with ID uc011agd.3_cds_0_0_chr22_15528159_f contains many (48) SNPs." I can't seem to find the column or exact location in the BED output that states this. 

Kind Regards,

Yvonne

galaxy ngs101 • 578 views
ADD COMMENTlink modified 2.0 years ago by Jennifer Hillman Jackson24k • written 2.0 years ago by yvonne.turquoise0
0
gravatar for Jennifer Hillman Jackson
2.0 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

It sounds as if you are using the original 101. Instead, try the updated version here: http://usegalaxy.org/galaxy101

The track datasets at UCSC do change (data is added, removed, and the like), so the exact same output will not always result when performing operations on them over time, but the overall method will produce similar results with the same scientific meaning in the content. By following the NGS101, you will learn techniques for using Galaxy and or performing some basic bioinformatics tasks.

This and other resources for learning Galaxy are listed at the top of the Support wiki page, with troubleshooting help below: https://wiki.galaxyproject.org/Support

Thanks! Jen, Galaxy team

 

ADD COMMENTlink written 2.0 years ago by Jennifer Hillman Jackson24k
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