removed rRNA tRNA in arabidopsis (using bowtie2)
Hello guys
I want to remove rRNA and tRNA in my RNA sequencing data
- How to remove rRNA and tRNA using bowtie2?
- Hw to download all plant noncoding RNAs from NCBI?
Please ASAP answer my question
Thank you
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Lee yujeong •
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Lee yujeong •
1 answer
Hi, can you ASAP check on internet, there is lot of information available regarding that.
- Pull down rRNA and tRNA fasta files,
- build a bowtie index.
- 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:
HTH
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