Subject: Query Regarding miRNA Sequence Alignment Outputs
Dear Cougarlj,
Thank you for sharing the pipeline with us. I have a question regarding the alignment outputs.
I used both Bowtie2 and COMPSRA-STAR to identify upregulated and downregulated miRNA sequences. However, I noticed some differences in the top dysregulated sequences between the two methods. Specifically, Bowtie2 generated counts for mature miRNA sequences, such as "mmu-miR-379-5p" or "mmu-miR-379-3p," while COMPSRA-STAR produced sequences like "mmu-miR-379," which seem to include precursor sequences as well.
Is there a way to configure COMPSRA-STAR to generate counts and alignments exclusively for mature miRNA sequences? Additionally, is it possible to use COMPSRA-STAR to discover novel miRNAs and quantify isomiRs?
Thank you in advance for your assistance.
Best regards,
Subject: Query Regarding miRNA Sequence Alignment Outputs
Dear Cougarlj,
Thank you for sharing the pipeline with us. I have a question regarding the alignment outputs.
I used both Bowtie2 and COMPSRA-STAR to identify upregulated and downregulated miRNA sequences. However, I noticed some differences in the top dysregulated sequences between the two methods. Specifically, Bowtie2 generated counts for mature miRNA sequences, such as "mmu-miR-379-5p" or "mmu-miR-379-3p," while COMPSRA-STAR produced sequences like "mmu-miR-379," which seem to include precursor sequences as well.
Is there a way to configure COMPSRA-STAR to generate counts and alignments exclusively for mature miRNA sequences? Additionally, is it possible to use COMPSRA-STAR to discover novel miRNAs and quantify isomiRs?
Thank you in advance for your assistance.
Best regards,