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Question: gene names from ucsc id
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gravatar for 1603.neha
2.5 years ago by
1603.neha • 70
1603.neha • 70 wrote:

i have cufflink and cuffdiff output. i want gene names in ncbi ids and a tabulated format. i can visualize them in IGV but how to export the data in text or tabulated format
mapping tophat rnaseq cuffdiff • 931 views
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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by 1603.neha • 70
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gravatar for Jennifer Hillman Jackson
2.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Tools in the group Text Manipulation can be used to isolate data columns, manipulate the format of content, remove header lines, and the like.

The assumption is that you used a reference annotation file containing the appropriate attributes when running these tools. If you didn't, consider that option. One source: http://support.illumina.com/sequencing/sequencing_software/igenome.html

There are ways to map UCSC transcript IDs to other identifiers, but this is not the most direct method.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k
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