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Question: How I can to remove specific sequence from a fungu of a plant-fungu interaction of total RNA-Seq data?
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gravatar for uli.arcos8
3 months ago by
uli.arcos8 • 0
uli.arcos8 • 0 wrote:

Hi, I am new in the field of the RNA-Seq and I am working with a plant-fungus interaction, but to the analysis I need to remove the fungus data of my total RNA-seq data.

My doubt is How I can to do it? and What software do you recommend me to do it?

Regards.
rna-seq galaxy hisat2 • 134 views
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modified 3 months ago by Jennifer Hillman Jackson ♦ 25k • written 3 months ago by uli.arcos8 • 0
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gravatar for Jennifer Hillman Jackson
3 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The fungi genome specific reads will fall out of the analysis during the mapping step to the plant genome.

Try using HISAT2 and set the output option to report unmapped reads to additional fastq outputs if you are interested in working with those later. That unmapped data will include both the fungi and any plant reads that didn't map, but you could map those against fungus genome(s) to filter.

The Galaxy RNA-seq tutorials cover HISAT2 usage in the context of an entire analysis, please see: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 3 months ago by Jennifer Hillman Jackson ♦ 25k
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