Hello
I am trying to screen small RNAs from sequencing data. The genome of the species is available but not well annotated and no microRNAs have been identified yet. I am trying to find homologous as well as novel miRNAs. I tried using tools like miReader etc. which gives me some results but I need to be sure. I tried mapping one dataset onto precursor sequences of mirbase which gave me 0 % overall alignment rate. Can someone please guide me as to what exactly should the parameters be for mapping. Also I need to filter any other ncRNAs using Rfam which is taking a lot of time. Will bowtie be good to use?
Getting 0% alignment rate when mapping your sequences to precursors in miRBase is a bit strange. Are you using raw sequencing data? If so, maybe the sequencing adapters are interfering there.
The only relevant parameter I used for BLASTing was just keeping alignments with e-value
Hi Oscar
The adapters are already trimmed. I did map my my data to Rfam first and then tried Shortstack which has given me some results. miRBase mapping still left. I will try your suggestion of Blast. Lets hope i get results.
thanks
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