how to annotate (rRNA, tRNA, Mt_rRNA, Mt_tRNA, etc) sequenced small RNA reads
Hi,
I have small RNA sequenced data. I annotated the small RNA sequenced reads against miRBase for miRNAs. I would like to annotate the sequenced small RNA reads into the following
mRNA_coding_sequence
rRNA
tRNA
mRNA_1000 TSS + 5UTR
mRNA_3UTR
Mt_rRNA
Mt_tRNA
misc_RNA
piRNA
snRNA
snoRNA
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you can do it with local NCBI blast against Rfam (for non coding RNAs) database and then grep according to each subtype