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ehk-kim / Dludoviciana

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U/D regulated homeobox genes #3

Open ehk-kim opened 3 weeks ago

ehk-kim commented 3 weeks ago

Send Jessie list of up/down regulated homeobox genes should be species | tissue | homeobox type | gene name

  1. get homeobox genes per species (separate files for each type)
  2. run find_common.py (/blue/barbazuk/kim.emily/d_lud/Orthofinder/analysis/upreg_genes) between the homeobox list & the upreg genes
  3. get output of sp_HOXtype_tissue_upreg.txt

module load python cd /blue/barbazuk/kim.emily/d_lud/Orthofinder/analysis/upreg_genes/ python find_common.py sp_tissue_upreg.txt /blue/barbazuk/kim.emily/d_lud/homeobox/sp_HOX_headers.txt /blue/barbazuk/kim.emily/d_lud/homeobox/sp_HOX_tissue_upreg.txt

  1. combine into 1 file with 2 columns: HOX type, gene per species per tissue

cat sp*tissue_upreg.txt >> sp_HOXgenes_tissue_upreg.txt

ehk-kim commented 3 weeks ago

accidentally overwrote all Dlud header.txt files. need to reobtain by parsing .out files

ehk-kim commented 3 weeks ago

go back and check deseq output (make sure that i have both upreg and downreg genes, aka the LFC)

upreg <- subset(res_sigs, log2FoldChange > 0); upreg leaf_upreg_genes <- rownames(upreg)

downreg <- subset(res_sigs, log2FoldChange < 0); downreg leaf_down_genes <- rownames(downreg)

note: can only make an inference about the tissue type that isn't the control ex) if gametophyte = "control" in deseq, can only make inference about the sporophyte