Question: HT-SEQ and edgeR installation
0
gravatar for jt008
2.9 years ago by
jt0080
jt0080 wrote:

Do you have HT-seq  and edgeR tools installed in Galaxy. If I want to get one, is it possible to get one.

thanks

ht-seq edger • 921 views
ADD COMMENTlink modified 2.9 years ago by Martin Čech ♦♦ 4.3k • written 2.9 years ago by jt0080
0
gravatar for Martin Čech
2.9 years ago by
Martin Čech ♦♦ 4.3k
United States
Martin Čech ♦♦ 4.3k wrote:

There are tools written by community that might be useful to you:

https://toolshed.g2.bx.psu.edu/view/lparsons/htseq_count
https://toolshed.g2.bx.psu.edu/view/fcaramia/edger
https://toolshed.g2.bx.psu.edu/view/amawla/edger

None of them is installed on Main though. You can install them on your own Galaxy (http://getgalaxy.org) or see whether some other public Galaxy has them: https://wiki.galaxyproject.org/PublicGalaxyServers

ADD COMMENTlink written 2.9 years ago by Martin Čech ♦♦ 4.3k
2

Unfortunately neither of the two edgeR tools in Martin's list will install automatically through your local production Galaxy admin interface so you will need to install them locally manually and then they will use the system installations of the edgeR packages breaking tool dependency chain reproducibility if the system administrator upgrades the system R/BioC installation without warning. It happens!

There are two packages in the test toolshed which install automatically to control their own tool dependency chains and work together pretty well - you get optional voom and deseq2 results to compare when you run the differential analysis. The htseq tool takes any number of bam files to produce a count matrix containing multiple samples and the edgeR tool takes those count matrixes and allows you to specify contrasts between any two arbitrary groups of samples, optionally adding a second GLM level if you need it (eg to model pairing between samples from the same animal):

https://testtoolshed.g2.bx.psu.edu/view/fubar/htseq_bams_to_count_matrix

and

https://testtoolshed.g2.bx.psu.edu/view/fubar/differential_count_models

There's a tutorial showing how those two tools work together in sections 4 and 5 of https://docs.google.com/document/d/1fQ1XfeOKhezJUDTzMXtZVY20c3RGoHe-HLvFOGzqU4s/pub and you may be able to try them out at http://galaxy-tut.genome.edu.au - understand that your work will be volatile there.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by fubar1.1k
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