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Old 02-01-2011, 01:05 AM   #1
Location: il

Join Date: Jun 2010
Posts: 64
Default small RNA seq analysis


I have small RNA seq data (plants).

I did the following:

1. remove adaptors (with cross match)
2. create tags

I now want to check which tags are known miRs and to get a list of miRs instead of tags (and for each miR have a record the relevant tags and total counts).

Would you use blast for this (tags vs. a database of the miRs)?
And write scripts that merges tags that "belong" to a miR?

Any suggestions on the percent identity and alignment length to use?

Any other suggestions?
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