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Old 10-15-2013, 06:29 AM   #1
paolo.kunder
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Default tag density distribution over the gene body

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
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Old 10-15-2013, 07:57 AM   #2
harryzs
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try ngsplot

https://code.google.com/p/ngsplot/
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Old 10-15-2013, 11:53 PM   #3
paolo.kunder
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Honestly I would like to avoid installing Galaxy in my server, any other suggestion?
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Old 10-16-2013, 01:25 AM   #4
Michael.Ante
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Hi Paolo,

have you tried Ensembl's Perl API in combination with the Bioperl's Samtools?
A nice tutorial can be found here.
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Old 10-16-2013, 01:47 AM   #5
harryzs
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Quote:
Originally Posted by paolo.kunder View Post
Honestly I would like to avoid installing Galaxy in my server, any other suggestion?
I don't think you need to install Galaxy.

Code:
 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.
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Old 10-17-2013, 08:26 AM   #6
paolo.kunder
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I think you need to install it,
anyway some other suggestions?
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Old 07-29-2014, 12:34 PM   #7
captainentropy
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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.
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