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6.8 years ago
Seq225
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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!!
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.