Hi,
I am wondering is there any way to extract read counts for each sample for novel microRNA predicted by miRDeep2. I could only find in the expressed_all_samples.csv file read counts for each sample for the known microRNAs but not for the novel ones. Did I missing something here? Thanks in advance for any kind of hint or help!
best, Dewi
•
written
by
sri.dewi •
1 answer
One method would be to first identify all the known and novel microRNAs in all of your samples pooled together (use the -d option with mapper.pl; and then use this output to run mirdeep2).
Next, create your own reference files using the novel and known miRNAs present in your samples. Then, you can run quantifier.pl for each sample using your custom reference fasta files rather than the miRbase ones.
I am not sure the best way yet to create the custom reference files.
Log in to answer this question.
-
How to deal with mirdeep2 output "miRBase miRNAs not detected by miRDeep2"
written by otieno43 •
-
Merging csv files with specific headers
written by windsur •
-
miRDeep2 sample read count different between mapper.pl and quantifier.pl
written by sg197 •
-
Possible reasons mapping percentage abysmally low for miRNA reads?
written by VBer
-
coordinates mature microRNAs from precursors
written by Amaranta_Remedios •
-
Generating read counts for my microRNA reads for a non model invertebrate
written by karthic
-
sRNA analysis by miRdeep2
written by mahfuz.290066 •
-
Novel MicroRNA prediction with Mirdeep 2.
written by gurjeetkaur268 •
-
miRNA analysis by miRDeep2
written by Xin
-
microRNA overexpression data
written by prosvirov.k •
