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#Alter this old command to pull out Gene ids corresponding to DEGs and store it in a file called DEG
sed 's/,/\t/g' deseq2_htseq_C1_vs_C2.csv|awk '{if ((($3>=1)||($3<=-1))&&($6<=0.05)) print $1,$3,$6}'|wc -l > DEG

#Command to pull out ALL gene ids and store it in a file called ALL
sed 's/,/\t/g' deseq2_htseq_C1_vs_C2.csv|cut -f 1 > ALL

##Command to pull out ALL gene ids, sorted by adjpvalue store it in a file called ALLRANKED
#Remember we already sorted our results by adjusted pvalue in the deseq2 script before writing it out to a file. So you#you just #needneed to pull out the gene ids in the order it already is in.
sed 's/,/\t/g' deseq2_htseq_C1_vs_C2.csv|cut -f 1 > ALLRANKED

#ON LS5: copy the path for the ALL and DEG filesALLRANKED file
pwd
 
#ON LOCAL COMPUTER: from a terminal tab 
scp <username>@ls5.tacc.utexas.edu:<pathtofileson/ALLRANKED> .