Hello all. I have been working with some very clean RNAseq data generated from Drosophila and have come across a few issues. First of all, I am using our local install of GALAXY - forgive me, but I am only a part-time bioinformaticist! That being said, I have used this interface for about five years now, so I am comfortable. The main issue troubling me right now is that I can use TOPHAT2 for mapping and am able to generate differential gene expression output using the Bowtie/Cufflinks/Cuffmerge/Cuffdiff pipeline. The problem is that the mapping is VERY low (about 50-60% for any of the fastqsanger files). I am only using clean data trimmed to 200bp or less (Ion Proton) with quality >20 median score. The problem is, when I use RNA-STAR I get multiple issues in the pipeline (problems with cufflinks that end up being problems in Cuffdiff that I don't want to get into here). What I want to know is, why do I get >80% mapped reads (and higher) when I use RNA-STAR, but only about 50% mapped reads with TOPHAT2? Is there some reason for this?
Thanks in advance. Working through this....
Thanks in advance. Working through this....
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