Alternative for GeneBody coverage from RseQC (Python) in R

Question

[Walter Baumann]

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

[zany1983]

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.

Answer 1

[michael.ante]

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