removed rRNA tRNA in arabidopsis (using bowtie2)

Question

[Lee yujeong]

Hello guys

I want to remove rRNA and tRNA in my RNA sequencing data

1. How to remove rRNA and tRNA using bowtie2?
2. Hw to download all plant noncoding RNAs from NCBI?

Please ASAP answer my question

Thank you

Answer 1

[Sukhi Singh]

Hi, can you ASAP check on internet, there is lot of information available regarding that.

1. Pull down rRNA and tRNA fasta files,
2. build a bowtie index.
3. Map your data to these indices and use

--un <path>           write unpaired reads that didn't align to <path>

Output will be a cleaned of r/tRNA sequences.

Other links :

• rRNA Removal In Rna-Seq Data
• http://seqanswers.com/forums/archive/index.php/t-32420.html​
• How To Annotate And Remove Rrna/Trna From Mirna Seq Data
• http://onetipperday.blogspot.de/2012/08/extract-unmapped-unpaired-reads-using.html​

2nd question:

• rRNA databases for plants
• http://www.ncbi.nlm.nih.gov/pubmed/25398903

HTH