Hey guys,
Paired-end reads data analysis of rna-seq is done. The report represents STAR aligner outperforms Hisat2 in uniquely mapped reads rates (however STAR is slower than Hisat2). >Scientifically reasoning< ; this is the core of the report, should be clearly and scientifically written. How to write that ?
Any hint or idea is appreciated
Besides I have the same experience with these tools, I just stopped using Hisat. Maybe you could evaluate what the reason is, e.g. examine some of the reads that mapped by STAR but not hisat? Given the current quality of sequencing we should expect >90% mapping rates. Some hypotheses (guess that is what you meant by reasoning) what could go wrong with hisat:
You can evaluate all these factors by doing some experiments.
I further think that speed is just a minor detail and should not be traded for accuracy.
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Please explain the problem better, what do you mean by Scientifically reasoning, honestly I have no clue what you mean and which 'report' you are referring to. Remember most people here are not taking the same course as you do. It sounds like an assignment, to post this here is just utterly ....
Analysis of 12 samples of human ( paired-end reads), mapping with STAR and Hisat2 results in some rates showing that Star maps higher rates of reads to the genome rather than Hisat2. I need to write a clear paragraph at the end of my report for those who refer to my report, explaining what exactly results are implying. For example 95% , 85%,96% in STAR and 75,76 and 78% rates using Hisat2. Ok, what next ? what is the main reasons behind those rates ? I need to know which factors I should take into consideration when writing the reasons.