Entering edit mode
10.5 years ago
liran0921
▴
150
Hi All,
After adaptor trimming, I can get the size distribution of small RNA using fastQC. And I have identified known and novel miRNAs using mirDeep2. But I am not able to the size distribution of the miRNA. Could anybody tell me how to get it? Thanks.
I think you should look for a local bio-informatician who wants to help you out. It will improve the quality of your research significantly
Thank you. I wish there is such bio-informatician in my center, but unfortunately not. That's why I came here to look for some help.
Ok, I will try to help you then. First you will have to clarify your question. Because your question is unclear, nobody bothered to offer you any help. At first, FastQC does not measure miRNAs, it is intended to do quality control on reads so it is unclearr what you have done. What is it you want to do right now? I guess you have a fasta file containing miRNAs and you want to get a distribution/histogram of their sizes?
I appreciate if you can help me. I have used mirDeep2 to identify known miRNAs. Now the problem is that mirDeep2 didn't produce a fasta file containing all the known miRNAs, although I can get the total counts of each known miRNAs. So I cannot get the size distribution statistics for known miRNAs if I don't have a table of the isomiR information of a fasta file containning all the known miRNAs. Could you tell me which software or method could perform this work? Thanks.
Ah I get it. What is the exact command you used for mirdeep2? And can you post a head (first 3 lines/rows) of the output table that mirdeep2 produced
Hi, I used the mirdeep2.pl to identify known miRNA and the mapper module to get the total reads counts for each miRNAs. Sorry that i don't know how to add figures of my results here. Anyway, the results are quite similar to their published papers where they show the results examples (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245920/figure/gkr688-F1/). As is shown in their figure 2, they produce a pdf file for each miRNA showing the isomiR alignment. But there is not a text file and no a single fasta file.
if you have used mirdeep2.pl you should have a file called results.csv. The first column of this file contains miRNA identifiers. Your problem boils down to looking up the sequence length of these identifiers so you can get their size distribution. Do you know how to do that?
I have this file. Actually, they have the total accounts for each known miRNA in this file, but how to get the length distribution of the total known miRNAs if you don't have the isomiR information of each miRNA?
Ok, so this is the thing I dont get probably. 1 miRNA can have multiple miRNA with varying lenghts? And you want to know what the lenghts are of each isomiR for each miRNA that is in your results.csv file?
In results.csv file, the total counts for each miRNA is summarized. But there is no info about the isomiRs for each miRNA. The isomiRs may vary in length, which is the reason why i cannot do the statistics now. If I can get the isomiR information, then i will know how to do it. Or there might be other solutions...