Hi I am generating a fasta file from a DESeq2 output in the following way:
bedtools getfasta -fi /son/genomes/mm10.fa -bed treatment_pw_padj.001_sorted.bed -fo treatment_pw_padj.001_sorted.fa
The above bed file has FDR information as a last column, I believe #12
I then run the following to search for instances of a specific motifs within these intervals:
fimo /son/MA0112.1.meme /son/treatment_pw_padj.001_sorted.fa
I get a list of located motif sites with p-values however I would like to preserve the DESeq2 FDR value located in the original bed file as well next to these newly filtered intervals, any ideas on how I could do that? Thank you.