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Old 01-05-2017, 04:09 AM   #21
Brian Bushnell
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That's pretty much as expected... on average, your miRNAs were 30 bp long, and virtually all (97%) of your read pairs overlapped.
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Old 01-05-2017, 04:26 AM   #22
GenoMax
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Originally Posted by mastercoder View Post
Hello again,

Here is the result I got from bbmerge, but i do not know how to interpret, if these overlapping in the middle or not. I feel illiterate. I also would like to ask you guys any documentation or any advice on how can I improve my self. Because there is nobody who is good at bioinfo where I am.

Go ahead and merge the R1/R2 files and then use the resulting single read representation for doing the mapping. Since you are mapping miRNA don't allow any gaps in the alignments.

You can use bbmap.sh for this purpose. I think @Brian has recommendations for miRNA alignment in bbmap thread or the help document included in bbmap distribution.

Note: If you want to be extra cautious you could pass the trimmed R1/R2 files through bbduk.sh with "tbe tpo" option and then merge them. That should get rid of any stray bases from adapters that may have remained behind.

Last edited by GenoMax; 01-05-2017 at 04:38 AM.
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Old 01-05-2017, 04:52 AM   #23
mastercoder
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Originally Posted by Brian Bushnell View Post
That's pretty much as expected... on average, your miRNAs were 30 bp long, and virtually all (97%) of your read pairs overlapped.
Okay, i will move forward to do mapping with BBMap. Thanks again. By the way this overlapping means, both R1/R2 have almost the same sequences? Thanks again.
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Old 01-05-2017, 10:54 AM   #24
Brian Bushnell
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Okay, i will move forward to do mapping with BBMap. Thanks again. By the way this overlapping means, both R1/R2 have almost the same sequences? Thanks again.
Yes, that's correct (in the overlapping region). Except that R2 is the reverse-complement of R1.
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