Dear great helpers,
I'm new in RNA-seq analysis and I am confused with the idea about filtering the rRNA contaminated sequences. Would you please kindly clarify me about these isssues?
1. I would like to known if it is routine work to filter out rRNA contamination in coding RNA-seq data and when should we do it.
2. Should we filter rRNA before or after alignment (some say we should perform filtering with bowtie before actual alignment with the prefered programs)
3. I'm working with various species, and I'm totally lost here what is the most common ways to perform such filtering. Some sample show me how to perform rRNA filtering in human or mouse but rarely mention about other species (I generally use Ensembl genome in work).
Thank you very much in advances for your great help,
Kaj
I'm new in RNA-seq analysis and I am confused with the idea about filtering the rRNA contaminated sequences. Would you please kindly clarify me about these isssues?
1. I would like to known if it is routine work to filter out rRNA contamination in coding RNA-seq data and when should we do it.
2. Should we filter rRNA before or after alignment (some say we should perform filtering with bowtie before actual alignment with the prefered programs)
3. I'm working with various species, and I'm totally lost here what is the most common ways to perform such filtering. Some sample show me how to perform rRNA filtering in human or mouse but rarely mention about other species (I generally use Ensembl genome in work).
Thank you very much in advances for your great help,
Kaj
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