Question: merging two bigwig files
3
gravatar for  DataFanatic
4.3 years ago by
DataFanatic270
DataFanatic270 wrote:

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,

bigwig chip-seq merge deeptools • 9.3k views
ADD COMMENTlink modified 4.3 years ago by Devon Ryan97k • written 4.3 years ago by DataFanatic270
7
gravatar for Devon Ryan
4.3 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

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.

ADD COMMENTlink written 4.3 years ago by Devon Ryan97k
3

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.

ADD REPLYlink written 4.3 years ago by Carlo Yague5.2k

Good point!

ADD REPLYlink written 4.3 years ago by Devon Ryan97k

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

ADD REPLYlink written 4.3 years ago by John12k
1

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.

ADD REPLYlink written 4.3 years ago by Devon Ryan97k
2

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.

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by igor11k

Nice!

ADD REPLYlink written 4.3 years ago by Devon Ryan97k
2
gravatar for Sinji
4.3 years ago by
Sinji3.0k
UT Southwestern Medical Center
Sinji3.0k wrote:

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.

ADD COMMENTlink written 4.3 years ago by Sinji3.0k
2
gravatar for igor
4.3 years ago by
igor11k
United States
igor11k wrote:

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.

ADD COMMENTlink written 4.3 years ago by igor11k
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