am using deep tools for TF (transcription factor ) ChIPSeq analysis, I used bamCompare to generate an input normalized IP bigwig file. Since I have 3 replicates of a treatment file can I merge this three to increase my signal intensity ?
Also , I received multiple fastq files from my core and I merged them using
cat *fastq.gz >> combined-In1.fq.gz
I later realized that people use bedtools merge to do this, is there a formatting problem if I used cat ?? Thanks,