remove rRNA/tRNA from miRNA seq data

[adam_ie]

Hi there, the rRNA sequences should be available in NCBI if your genome is sequenced - and get your tRNA sequences from Rfam, which is available through Biomart here: http://xfam-biomart.sanger.ac.uk/ - download the tRNA sequences for your genome.

Then create a multi-FASTA file with all the rRNA and tRNA sequences inside it, build a Bowtie index of this multi-FASTA file, and align your reads against it.

You can keep the unaligned reads then which do not map to rRNA or tRNA.

For example:

bowtie --best --un <unaligned_reads_file.fq> index_of_rRNAs_and_tRNAs <input_fastq_file>

That should do the trick, then align unaligned_reads_file.fq against your genome.

[lran2008]

I am really stuck here. It would be quite helpful if anybody can provide me some examples on how to blast against Rfam.

[lran2008]

Hi All,

I am beginner at miRNA analysis. Now I am working on miRNA annotation.I have been working on it for several days but still have no idea how to do it.
What I want is to annotate and remove rRNA/tRNA from my total data. Could anybody give me some guidelines or provide some resources?

I know I should blast against Rfam. And probably I should use blastn. But I haven't been able to get what I mentioned above. I would appreciate if somebody can help me on it.

Thanks!