Hi,
I conducted a RNA-seq run for microRNAs. I was wondering if there is a workflow to analyze (initially) the data in Galaxy. All the files are in fastq format. I would like to remove the adaptor sequences and then map them to the bos taurus and see if there is differential expression among time points. I know there is miRanalyzer but am not sure how to have the data processed before running in that program. Any help would be greatly appreciated! Thanks!
use iMir. It takes fastq files as input, remove adapters, identify known and novel miRNAs (miRanalyzer, miRDeep2) and perform differential expression analysis automatically.
Here is the link of paper.
http://www.biomedcentral.com/1471-2105/14/362
use iMir. It takes fastq files as input, remove adapters, identify known and novel miRNAs (miRanalyzer, miRDeep2) and perform differential expression analysis automatically.
Here is the link of paper.
http://www.biomedcentral.com/1471-2105/14/362
It is possible to run miRdeep2 in Galaxy and you can install it from the test-toolshed if you are an administrator. I however preferred to run it through command line as it was a struggle to set it up in galaxy. Maybe the recent versions of mirdeep2 in test-toolshed are easier to set up though.
Are you sure that miRanalyzer (now known as sRNAbench) won't work for you? If you use the web interface, It expects the reads to be in fastq format but gzipped (i.e. .fq.gz or .fastq.gz). That's worked well for me for removing adapter sequences and mapping for human, mouse and rat microRNAs. Of course, once you have your microRNAs mapped and read counts assigned you'll need something like DESeq or edgeR to gauge differential expression between time points.
https://hyperbrowser.uio.no/mircandref/
enable advanced settings and you cna upload your genome instead of genomic reads.
Check out http://www.nature.com/natureevents/science/events/47533-microRNA_Analysis_Using_Next_Generation_Sequencing
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