Question: removed rRNA tRNA in arabidopsis (using bowtie2)
0
gravatar for Lee yujeong
4.3 years ago by
Korea, Republic Of
Lee yujeong0 wrote:

hello, guys

 

i want to remove rRNA and tRNA in my rna sequencing data

1 .how to remove rRNA and tRNA using bowtie2?

2 .how to download all plant noncoding rnas from NCBI?

 

please ASAP answer my question 

Thank you 

ADD COMMENTlink modified 4.3 years ago by Sukhdeep Singh9.9k • written 4.3 years ago by Lee yujeong0
0
gravatar for Sukhdeep Singh
4.3 years ago by
Sukhdeep Singh9.9k
Netherlands
Sukhdeep Singh9.9k wrote:

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 :

2nd question:

HTH

ADD COMMENTlink modified 4 days ago by RamRS24k • written 4.3 years ago by Sukhdeep Singh9.9k
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