I have mi-RNA sequencing data, where my 3 prime adapter is attached with 12 Nucleotide UMI Sequence (in random manner) along with Reverse Transcriptase primer and Universal Adapter
Overall sequence pattern= miRNA+3Prime adapter+RT primer+Universal Adapter
I am trying to remove the UMI sequence using UMI tools. I have also looked in to the regex function in UMI tools but i am not sure it will work because of the sequence pattern i have.
Please let me know if i have any chance of processing the sequence with UMI tools.
I have attached an example of my sequence pattern
Image annotation: 3 prime adapter colored in RED
Reverse Transcriptase primer in Orange
and in between them is the 12 Nucleotide UMI bases.
And after Reverse Transcriptase primer is Universal Adapter.
I don't understand what you are trying to say in text and in figure, its too confusing. Can you please describe again in a simpler way?
Why dont you just mark in image what you want to remove, and do you have any particular sequence (for UMI) that is uniform in your data?
The answer's can be found here :
https://www.biostars.org/p/358303/#358523
Rajesh Pal In the discussion I concluded that if one can't explain what he/she want to do, its hard to give right answer.
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