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Question: Gene names from 3'UTR sequencing reads
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gravatar for j.foster
2.6 years ago by
j.foster • 0
j.foster • 0 wrote:

Hi, I have some sequencing reads from iCLIP data of 3'UTR sequences. This is in a .reads.bed file in the following format:

1 2 3 4 5 6

chr3 60745142 60749648 1 3 -

chr8 121548452 121548571 6 1 -

etc.

Column 1 being the chromosome, and 2 and 3 being the genomic location.

What tool(s) can I use in galaxy to give me the names of the genes that these 3'UTR genomic intervals are located in?

Thanks,

John
rna-seq galaxy • 775 views
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modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.6 years ago by j.foster • 0
1
gravatar for Mo Heydarian
2.6 years ago by
Mo Heydarian ♦ 830
United States
Mo Heydarian ♦ 830 wrote:

Hi John,

One way to link your 3' UTR coordinates to gene names would be to get the appropriate transcript coordinates for your organism from the UCSC Table Browser (Get Data -> UCSC Main Table Browser) and use the 'Join' tool (Operate on Genomic Intervals -> Join) to link your coordinates with the annotated coordinates (and gene names).

You have the option in the UCSC Table Browser to import full gene annotations (coordinates) or just the features you are interested in (3' UTR exons).

Cheers,

Mo
ADD COMMENT • link written 2.6 years ago by Mo Heydarian ♦ 830
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