Hello,
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?
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?
