tag density distribution over the gene body

[paolo.kunder]

Dear All,

I have a bam file of a MeDIP seq sample.
I have also a bed file of all mouse genes.

I would like to plot the tag density over the genebody as illustrated in this two examples I found in the literature.

I know how to plot the tag density distribution relative to the TSS and +2kb/-2kb both, but how do I deal with the gene body?

Many Thanks,
Paolo

[harryzs]

try ngsplot

https://code.google.com/p/ngsplot/

[paolo.kunder]

Honestly I would like to avoid installing Galaxy in my server, any other suggestion?

[Michael.Ante]

Hi Paolo,

have you tried Ensembl's Perl API in combination with the Bioperl's Samtools?
A nice tutorial can be found here.

[harryzs]

Honestly I would like to avoid installing Galaxy in my server, any other suggestion?

I don't think you need to install Galaxy.

 A user only needs to write a very small configuration file, telling the program which samples to look at and how they should be combined with different regions, and then run the program with one command line. A web-based version (Galaxy) of ngs.plot is also developed to be used by wet-lab biologists who tend to be averse to command line usage.

[paolo.kunder]

I think you need to install it,
anyway some other suggestions?

[captainentropy]

No, you don't need Galaxy. What harryzs posted (directly from the ngsplot website) is correct.

I'm using ngsplot and I do not have Galaxy installed on my server.