Which one is preferable in NGS? Using different software for secondary and tertiary analyses or using one complete software package for both of the above? Waiting for some lights to be thrown of.............
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software
There is no such thing that one tool/ software for all your needs. I have seen people doing mistakes. It will depend on what your questions are e.g in Chip seq histone modification and transcription factor are two different kinds of analysis though basic concept is similar (in layman- no of reads in a particular region) -
Hey Honey.. Thnx for your getting back on this.. I put the question from a different point of view..You have two options to go for:
1. You have a suite/ soft package which performs all basic analyses before going downstream, say, de novo assembly or reference guided alignment etc and also doing all those downstream analyses you are concern about (as you said, ChIP, gene expression analysis) in a interoperable manner.
2. You have to use a software for performing assembly, alignment etc and a different software for your concerned downstream experiment.
So, which one you would go for? A soft package or different soft?
So far I think, there may be some compatibility issues between output of a software and input of next required software, which have to be solved by some conversion tool.
Don't you think here researchers may face some troble in converting the formats?Comment
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