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Strand-specific resolution of ribosome profiles
06-May-2015, 07:14 AM (This post was last modified: 06-May-2015 07:16 AM by Renana.)
Post: #1
Strand-specific resolution of ribosome profiles
Hello,

Could you please help me with the following query:

In my understanding, at UCSC everything is referenced related to positive strand coordinates even for negative strand items. Is there an option in your database to check from which strand the read arose? Assume a gene is located on the positive strand and another gene is located on the corresponding coordinates on the negative strand. In this case, how can I tell from which strand the read arose?

Any comments would be appreciated.

Thanks,
Renana
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06-May-2015, 08:39 AM
Post: #2
RE: Strand-specific resolution of ribosome profiles
Hello Renana,

Regarding your query about the strand specificity of the read alignments, unfortunately in the current implementation the strand orientation is not provided. For example, in the Table Browser the strand orientation of the mappings is not listed.

However, if the region is annotated then the strand can be obtained by clicking on the transcript annotation. But if you are exploring a region with overlapping genes on opposite strands, this approach will not help.

This is something we want to improve and we will work on trying to provide the strand information.

Thanks for your suggestion.
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