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 ??
I'm going to echo what the others have said and say that while it's certainly possible to merge the bigWig files (you can't do this with cat), I wouldn't recommend it (N.B., I'm one of the deepTools authors, if that makes it more convincing). It's generally best to look at or further process the samples as individual entities, which helps in conveying the biological variability.
If you really want to merge the bigWig files then you can use bigWigMerge from UCSC tools.