What organism's genome should be used in FastQ Screen

Question

[phamh]

Hi,

I have 6 Physomitrella patens cDNA libraries and want to run FastQ Screen on CyVerse to see if there's any contamination. So far, I've decided to use human reference genome because there could be human DNA contamination during the prepping process. I also want to use bacteria and fungi reference genome, but I'm not sure specifically which species to look for. How do I know this? Where should I start?

Thank you.

[andres.firrincieli]

Hi,

is this a differential gene/transcript expression study? If so, I would not worry to much about the contamination, just map your RNA-seq reads on the reference genome/transcriptome for quantification of gene/transcript expression.

[phamh]

Thank you for your help. May I ask why I don't have to worry about contamination?

[Tm]

During mapping process any reads originating from any other source will not map to Physomitrella patens genome and thus contamination will be removed automatically. If you get very less % mapping on Physomitrella patens genome then in that case you can extract unmapped reads and denovo assemble it followed by blast against NCBI NR/uniprot database.

[Tm]

I agree with andres. Still if you want to check contamination better consider model plant, fungal and bacteria genomes.

[phamh]

Thank you for your help.