Question: Alternative for GeneBody coverage from RseQC (Python) in R
1
gravatar for Walter Baumann
15 months ago by
Walter Baumann10 wrote:

Hi,

There is a function called geneBody_coverage.py in the Python tool RseQC, which determines whether the coverage of Reads is uniform along the transcripts, o if there is a 3' or 5' bias.

Now I want to apply this tool to my research question: I want analyse my coverage within the 5'UTR. However, due to the fact that the 5'UTR of each transcript is different, I have to normalize it first. So in the end I want to have a plot with "Percentile of 5'UTR" on the x-axis and "Read number" on the y-axis.

Does anyone of you know a convient alternative for performing this analysis in R? I already have my bam file in R (imported via "readGAlignments")+ I searched all 5'UTRs with "fiveUTRsByTranscript".

Thanks for any ideas

rna-seq R • 649 views
ADD COMMENTlink modified 13 months ago by michael.ante2.5k • written 15 months ago by Walter Baumann10

I also want to know that! what I exactly want to do is do "normalized coverage analysis along given intervals". for my given intervals of my interested(bed file),with varied length, I want to plot normalized mean coverage along these intervals. and further,I want to compare if there is difference is coverage depth and width on different groups of intervals.

ADD REPLYlink written 13 months ago by zany198310
1
gravatar for michael.ante
13 months ago by
michael.ante2.5k
Austria/Vienna
michael.ante2.5k wrote:

Hi Walter,

You can provide the 5' UTRs as a bed-file to the RSeQC tool.

Alternatively, you can have a look at the TSS example of the Htseq python library here . You need to tweak a bit around, but it's very easy adaptable.

Cheers,

Michael

ADD COMMENTlink written 13 months ago by michael.ante2.5k
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