About isomiRs counts

[palbioinfor]

Hi Lorena,
Thanks once again for this useful package. I have a question which is more biological I guess. So, after getting the counts file if I look at the mature miRNA (ref) and isomiRs separately (not as merged) , I notice that almost all isomiRs (like 95%) are more abundant than mature miRNAs (ref). They have more raw read counts than mature ones.Biologically, it seems like it should not be the case. My team and I are little concerned about it . Can you share your idea on this?

[lpantano]

HI, Actually that is not that rare, if you divide by different isomiR type, probably you’ll see that changes at 3’ are ones that are quite expressed as well. If you add all isomiRs is easy to be higher than the reference, if you separate by isomiR type, then you’ll see that sometimes reference is the most expressed but not always and that depends on the sample type. I hope this help. I am happy to look at some examples if you want.

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On Jul 23, 2018, at 8:37 PM, palbioinfor ***@***.***> wrote: Hi Lorena, Thanks once again for this useful package. I have a question which is more biological I guess. So, after getting the counts file if I look at the mature miRNA (ref) and isomiRs separately (not as merged) , I notice that almost all isomiRs (like 95%) are more abundant than mature miRNAs (ref). They have more raw read counts than mature ones.Biologically, it seems like it should not be the case. My team and I are little concerned about it . Can you share your idea on this? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#12>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABi_HJ_Pqr381gNkCM_z2wsWyrNCTyc6ks5uJmxJgaJpZM4Vb5oc>.

[palbioinfor]

Thanks a lot for your reply.
I would be happy to show you an example

I found many like this.
Also, should I abandon the orphan isomiRs where there are no reference miRNA had been annotated? I found a lot of orphan isomiRs and if I remove them I will be left with very less number of mature miRNA and their isomiRs.

[lpantano]

Hi, I think is ok what I am seeing. I won’t remove the orphan isomiRs if they add up to a good amount of counts. Just to make sure there is not bugs there I would use isoSelect to get all the sequences for these miRNA you sent, so you can check the exact sequence this high expressed isomiR you see here and double check with the mature sequence you used for the annotation. I hope this helps!

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On Jul 31, 2018, at 5:13 PM, palbioinfor ***@***.***> wrote: Thanks a lot for your reply. I would be happy to show you an example <https://user-images.githubusercontent.com/36253759/43487447-a8b980dc-94e4-11e8-9baf-c375c94d074c.png> I found many like this. Also, should I abandon the orphan isomiRs where there are no reference miRNA had been annotated? I found a lot of orphan isomiRs and if I remove them I will be left with very less number of mature miRNA and their isomiRs. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#12 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABi_HBsABOYL4_p83zKYEEIfvTaALYqkks5uMMhmgaJpZM4Vb5oc>.

[ningb]

Hi Lorena,
Thank you so much for developing such a useful package.
One follow-up question on this thread. I have no issue navigating around the manual. However, is it possible to generate a isomir count table from the object, ie row for each type o isomir and column for each sample?

Best,
Boting

[lpantano]

Hi, Thanks for trying the package :) you should be able to do that with the function isoCounts and turning to TRUE all the parameters: http://lpantano.github.io/isomiRs/reference/isoCounts.html Let me know if that works. Cheers

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------------------------- Lorena Pantano, P.h.D Research Scientist Biostatistics Department Harvard T.H. Chan School of Public Health https://mirtop.github.io https://lpantano.github.io

On Fri, Mar 22, 2019 at 5:22 PM ningb ***@***.***> wrote: Hi Lorena, Thank you so much for developing such a useful package. One follow-up question on this thread. I have no issue navigating around the manual. However, is it possible to generate a isomir count table from the object, ie row for each type o isomir and column for each sample? Best, Boting — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#12 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABi_HGdQF5fCKDbRyIOVQzasgEj6YSozks5vZUmsgaJpZM4Vb5oc> .