Question: how to annotate (rRNA, tRNA, Mt_rRNA, Mt_tRNA, etc) sequenced small RNA reads
0
gravatar for bioinforesearchquestions
9 days ago by
United States
bioinforesearchquestions120 wrote:

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

ADD COMMENTlink written 9 days ago by bioinforesearchquestions120
1

you can do it with local NCBI blast against Rfam (for non coding RNAs) database and then grep according to each subtype

ADD REPLYlink written 9 days ago by Sam50
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