How to separate small RNA reads that show 10nt overlap?
I want to separate the reads from my small RNA library that show a specific overlap (i.e. 10nt). Idea is to separate all my reads that were generated by the ping-pong piRNA pathway. Is there any way?
I am using a python script developed by Institut de Biologie Paris Seine at: https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature
This extremely useful script gives me Z-scores for all overlaps but I want to separate out the reads of a specific overlap. I am not a coding guy who can write some extra lines and get it done.
So, How can I get my reads?
Thank you very much!!
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Can you add information about what kind of data you have? 10nt overlap with what? Also the link you pasted above appears broken.
It's a small RNA library (fastq file, produced by illumina sequencing). The piRNA class small RNAs show a 10nt overlap between forward and reverse strand if they are produced by ping-pong mechanism. The entire small RNA library has all sort of reads (size ranges 18-31nt) belonging to miRNA, siRNA, and piRNA. piRNAs could be generated in so-called ping-pong mechanism or primary pathway (which would not show a 10nt overlap). I want to separate the reads from the entire library that show 10nt overlap. I have been using a python script that has been very useful to me. It produces z-scores for every possible overlap among the reads. However, I am not sure if it can be manipulated to separate the reads that show a specific overlap (like 10nt).
Sorry about the link. Hope it works this time! https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature
You may want to take a look at a couple of pipelines for piRNA analysis mentioned here.
Thanks. Your link seems very useful!
Hello mosharrofgeb!
It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?p=209068
This is typically not recommended as it runs the risk of annoying people in both communities.
I thought different sites have different viewers. Anyway, I tried to delete one from the other site. For some reason I couldn't find the option. I will contact their admin. Thanks.