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SMR || RNA seq data || BESD format .epi physical position

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complexgenome
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SMR || RNA seq data || BESD format .epi physical position May 18, 2020 15:27:23 GMT

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Post by complexgenome on May 18, 2020 15:27:23 GMT

Dear GCTA devels,

I'm interested to use SMR using eQTL analysis from RNA-seq data. I create besd file format using eQTL matrix format.

However, what should be the position in .epi file for gene from RNA-seq eqtl analysis? Gene has start as well end position.
If it were micro-array then probe position makes sense.

Thank you.

ax New Member Posts: 27	SMR \|\| RNA seq data \|\| BESD format .epi physical position Jun 22, 2020 5:53:27 GMT Quote Select Post Deselect Post Link to Post Member Give Gift Back to Top Post by ax on Jun 22, 2020 5:53:27 GMT Yes, the position in the .epi file should be the probe position.

complexgenome New Member Posts: 4	SMR \|\| RNA seq data \|\| BESD format .epi physical position Jun 24, 2020 14:17:40 GMT Quote Select Post Deselect Post Link to Post Member Give Gift Back to Top Post by complexgenome on Jun 24, 2020 14:17:40 GMT Thanks. What is commonly used - start or the end position of the Gene while conducting the analysis?

ax New Member Posts: 27	SMR \|\| RNA seq data \|\| BESD format .epi physical position Jul 6, 2020 4:08:02 GMT Quote Select Post Deselect Post Link to Post Member Give Gift Back to Top Post by ax on Jul 6, 2020 4:08:02 GMT That's the mid position of the probe.

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