Chiseq files for deseq2

Question

[CL]

Hello everyone, I have 4 peaks bed files and i want to create count matrix for analysis in deseq2 I want to see the difference acetylation between them, I want in the column the 4 samples, and in the rows peaks I understand i can make it by using this function:

featureCounts -p -O -T 8 -a $gtf -o $outfn --extraAttributes gene_name -Q 10 $*

But i am not sure how to do that, I am really confused and i would like to get any details about that

Thanks!!

[Darked89]

Check the SAF format in the manual: https://subread.sourceforge.net/SubreadUsersGuide.pdf You will need to convert the BED files into a format compatible with featureCounts. SAF is simpler than GTF but some scripting will still be required. Last but not least: some peaks in your four BED files may be identical or overlap with peaks from other files. You will need to decide how to treat these overlapping peaks. BTW do you also have input/control BAMs?