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How to plot "normalized read density" vs "insert size"

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
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updated by karl.stamm karl.stamm • written by dec986 dec986

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!

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written by Michael Dondrup Michael Dondrup

hello Michael,

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

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written by dec986 dec986

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".

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written by Michael Dondrup Michael Dondrup

1 answer

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.

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written by karl.stamm karl.stamm

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