Question: (Closed) How to plot "normalized read density" vs "insert size"
0
gravatar for dec986
3.4 years ago by
dec986210
United States
dec986210 wrote:

Hello,

I've been requested how to make a plot Plot like this, which is from an ATAC-Seq methods paper (Buenrostro, J.D., et al. doi: 10.1002/0471142727.mb2129s109) of RNA-Seq Data I'm not sure how I can get the insert size and then the normalized read density. I've tried rseqc's insertion_profile.py but there are bugs in that script so I can't use it.

How can I go about making getting this data from fastq or aligned bam files?

rna-seq • 1.3k views
ADD COMMENTlink modified 3.4 years ago by karl.stamm3.6k • written 3.4 years ago by dec986210

Hello dec986!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink written 3.2 years ago by Michael Dondrup47k

hello Michael,

this was an accidental double post. I tried to delete this thread but didn't see how.

ADD REPLYlink written 3.2 years ago by dec986210

Sometimes this happens if the the Add button is pressed twice, the Add process is in need of a semaphore preventing more than a single post per click. The delete option is found under "moderate".

ADD REPLYlink written 3.2 years ago by Michael Dondrup47k
0
gravatar for karl.stamm
3.4 years ago by
karl.stamm3.6k
United States
karl.stamm3.6k wrote:

You can plot values using the plot() command in R. Just put in your x and y values of interest like

plot(x,y)

and it will make a nice scatter-diagram.

If youre having trouble getting the insert size values, ask a question about them specifically.

If youre having trouble getting the "normalized read density" values, ask a question about them specifically.

If youre having trouble with "rseqc's insertion_profile.py", ask a question about it specifically.

I think you're confused about several issues and should take some time to slow down, break apart the problem and exercise some problem solving skills.

ADD COMMENTlink written 3.4 years ago by karl.stamm3.6k

Devon Ryan gave a very good response here: C: How to plot "normalized read density" vs "insert size"

I accidentally double posted, had issues uploading the image. I don't know how I can delete this question.

ADD REPLYlink written 3.4 years ago by dec986210
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