extract rRNA/tRNA and other ncRNA ratio in a table from small RNA-seq

Question

[Rey]

Hi all, I have some small RNA-seq libraries from some plants. I downloaded ncRNA from Ensemble Plants as I don't know how to use the Rfam database. How could I extract the rRNA/tRNA and other ncRNA ratios in a table? I am using this code: bowtie ncRNA -f unique_tags.fa -S unique_tags.ncRNA.sam --un unique_tags.unaligned.ncRNA.fa --al unique_tags.aligned.ncRNA.fa the result I got is:

1_x9 CACGGCCTGATCAAATCG 2_x8 ACATCGAGTAGACCCTGT 6_x7 TAATTCATGATCTGGCAT 7_x7 GCAAAGATCGTCTTATTC How can I interpret these results? Thank you!