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2.7 years ago
gallicchiolorenzo
▴
10
Hi all :)
I am working with smallRNA sequencing data and I have produced bam file containing the reads that map to microRNAs in drosophila melanogaster. Now I would like to produce a count table in order to perform differential analysis. Which is the tolls that best suits my stage? I was looking into miRdeep and mirPRo but I was wondering if there is something faster as I already have the bam file.
The major issue that I am encountering seem to be some formatting as both mirPRo and miRdeep do not like the formats that my file have. They are also having some issues reading fasta or gif files from miRbase...
If you have a pipeline to suggest that would be great!
Thanks :)
