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junchaoshi / sports1.1

Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs
GNU General Public License v3.0
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can we merge the similar sequences when processing the smallRNA data #29

Closed sunhaifeng123 closed 1 year ago

sunhaifeng123 commented 1 year ago

Hi, Junchao,

I got the results from sports1.1, some similar sequences like:

AAAAAACATTAGACTGTGAATCTGACAACAGGAAATAAACCTCCT 42 30 232 53 296 24 46 104 197 229 AAAAAACATTAGACTGTGAATCTGACAACAGGAAATAAACCTCC 16 9 63 22 120 12 16 20 48 30 AAAAAACATTAGACTGTGAATCTGACAACAGGAAATAAACCTC 29 3 41 22 47 7 4 0 21 21

and my supervisor hope that I can merge such three sequence to one so that perfrom following differential analysis.

I don't know whether it's suitable here for smallRNA data process and I didn't find literatures with such a description.

Can you give me some ideas or suggestions?

Thank you very much in advance!

Best, Haifeng Sun

Ph.D. candidata student from Nanjing Medical University, China

junchaoshi commented 1 year ago

Hi Haifeng,

It depends on the reason for merging these sequences. Are these sequences share similar functions? Some previous works (e.g., PMID: 23063653) have shown that some miRNAs with different length, although sharing the overlapping sequences, have distinct seed sequences and target specificity. Hope the information helps.

I have to close the issue since it's not related to the software.

Best, Junchao