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hputnam / Becker_E5

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Clarify the Annotation file #13

Closed hputnam closed 4 months ago

hputnam commented 4 months ago

This file needs to have 27,439 genes to match all in the genome paper, even if genes did not have any hits

daniellembecker commented 4 months ago

Look into creating of pver_GOterms_interprot_swissprot_blast_trembl_20211203.csv file to see why genes aren't matching full annot file

daniellembecker commented 4 months ago

https://github.com/hputnam/Becker_E5/blob/master/Functional_Annotation/Scripts/pver_annot_compile.Rmd

daniellembecker commented 4 months ago

https://github.com/hputnam/Becker_E5/blob/master/Functional_Annotation/2021-12-08-Molecular-Underpinnings-Functional-Annotation-Pipeline.md

daniellembecker commented 4 months ago

Solved why the pver_GOterms_interprot_swissprot_blast_trembl_20211203.csv file had less then 27,439 genes, it was due to NA filtering in the https://github.com/hputnam/Becker_E5/blob/master/Functional_Annotation/Scripts/pver_annot_compile.Rmd script, I have now commented out the na.omits from the script. However, there are still inconsistent gene naming issues I am addressing in issue #14