merging two bigwig files

Question

[ATCG]

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,

Answer 1

[Devon Ryan]

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.

[Carlo Yague]

I agree, merging replicates shouldn't be used to "increase signal intensity" as the OP said. However it can be used to summarize data, for instance for visualization in a genome browser where too many tracks can be confusing. In fact, I use bigWigMerge quite often for that purpose, but only after doing all the statistical analysis with the unmerged replicates.

[Devon Ryan]

Good point!

[John]

Can genome browsers not combine/merge tracks in this way through their interface? I've never needed to do this so i've never checked

[Devon Ryan]

IGV can group tracks together, but I don't think it can sum the values (at least on the fly, there might be some tool for that). There's a genome browser from the Babraham (SeqMonk) that can do a lot of crazy stuff stuff like that, I think.

[igor]

IGV can add, subtract, multiply, and divide tracks. Go to Tools > Combine Data Tracks.

I think this feature was added in the last year or two. I searched for this a while back and couldn't find it.

[Devon Ryan]

Nice!

Answer 2

[Sinji]

It's better to merge the three BAM files using Picard's MergeSamFiles and then use Deeptools to create a new bigWig file.

Using cat is fine, bedtools merge does not do what you think it does.

Answer 3

[igor]

Yes, you can technically merge the FASTQs with cat.

However, you probably don't want to do this. You should keep your replicates separate so you can check for how reproducible the signal is.