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Question: RNA seq analysis of host pathogen dataset
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gravatar for wass.mark
3.3 years ago by
wass.mark • 0
United Kingdom
wass.mark • 0 wrote:

Hi,

I have an RNAseq dataset that contains data for a host and a parasite, one run of the host alone and one that combines the host and parasite.

What would be the best way of analysing the data? I would like to

1. Identify what paraiste proteins are expressed

2. Identify changes in expression with the parasite infected.

 

Many thanks,

Mark
rna-seq • 751 views
ADD COMMENT • link •
modified 3.3 years ago by frederik.coppens • 40 • written 3.3 years ago by wass.mark • 0

Do you have a annotated reference genome?

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

Yes there are annotated reference genomes for both host and pathogen

ADD REPLY • link written 3.3 years ago by wass.mark • 0
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gravatar for frederik.coppens
3.3 years ago by
frederik.coppens • 40
VIB, Gent, Belgium
frederik.coppens • 40 wrote:

if there is little sequence similarity between host and parasite (which I assume is the case) you can use a default RNA-seq pipeline to analyse it as Bjoern mentioned. I would do two separete analyses then: with the host ref genome and with the parasite ref genome. 

If you also do both for the host-only dataset, you will also get an idea of how many reads from your host would map to your parasite genome. If this "cross-mapping" would be problematic, you could make an artificial ref containing both the host and parasite (and e.g. only consider unique mapping as a start point)

Frederik

 
ADD COMMENT • link written 3.3 years ago by frederik.coppens • 40
1
gravatar for Bjoern Gruening
3.3 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi!

I don't see why you can not use a normal RNA-seq pipeline.

Have a look at the Galaxy 101 tutorial: https://wiki.galaxyproject.org/Learn/GalaxyNGS101 or our small RNA-seq tutorial at github: https://github.com/bgruening/training-material/tree/master/rna-seq

Cheers,

Bjoern
ADD COMMENT • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

Hi,

Yes I tend to agree, my thought is how I should do it when for the set that contains the host/pathogen transcripts. Do I align to the host first and then align anything else that isn't aligned to the pathogen genome? Is this a reasonable thing to do?

Thanks, Mark

ADD REPLY • link written 3.3 years ago by wass.mark • 0

Yes, this is how would do it :) ... but this does not mean much ...

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k
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