Question: How to plot "normalized read density" vs "insert size"
0
gravatar for dec986
3.7 years ago by
dec986230
United States
dec986230 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? EDIT:

rna-seq • 2.4k views
ADD COMMENTlink modified 3.6 years ago by ATpoint36k • written 3.7 years ago by dec986230

Please don't post the same question in duplicate threads: How to plot "normalized read density" vs "insert size"

ADD REPLYlink written 3.7 years ago by genomax85k

sorry, the image attachment wasn't working, I didn't realize that I double posted. I don't see how I can delete that question.

ADD REPLYlink written 3.7 years ago by dec986230

That is ok this time. Since the other question has a different answer I don't want to delete it.

ADD REPLYlink written 3.7 years ago by genomax85k
3
gravatar for Devon Ryan
3.7 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

Try bamPEFragmentSize from deepTools.

ADD COMMENTlink written 3.7 years ago by Devon Ryan96k

Hi Devon,

sorry about the late reply (too many things to do) but this doesn't enter image description here generate the correct x axis ('insert size' vs 'fragment length'). Perhaps this is enough?

ADD REPLYlink written 3.6 years ago by dec986230
1

Insert size and fragment length are the same thing.

ADD REPLYlink written 3.6 years ago by Devon Ryan96k

thank you Devon, you have been very helpful!

ADD REPLYlink written 3.6 years ago by dec986230
0
gravatar for ATpoint
3.6 years ago by
ATpoint36k
Germany
ATpoint36k wrote:

This plot was generated simply by applying CollectInsertSizeMetrics from Picard tools to the filtered bam file (removed chrM, MAPQ>int as you like, properly-paired only if you like, remove duplicates) and divide the obtained counts by the number of reads in the bam.

Just out of curiosity, what do you mean by "of RNA-seq data" in your question? This plot reflects the fragment sizes generated by the transposition of open chromatin regions; nothing to do with RNA at all.

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by ATpoint36k

"of RNA-seq data" means that dec986 has RNAseq data rather than ATACseq. This is also why the plot dec986 posted has such long apparent fragment lengths, since there's splicing.

ADD REPLYlink written 3.6 years ago by Devon Ryan96k
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