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Old 03-20-2020, 01:24 PM   #1
Whattodo
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Location: Croatia

Join Date: Mar 2020
Posts: 1
Default What RNAseq mapper to use?

Hello everyone,

I am dealing with NGS data for the first time, so I am very new to everything. When I was looking for a read mapper for my RNAseq data I was a bit confused on which one is "the best" for me.
My data consists of 30 samples each of ~3GB in size, that contain paired-end 150bp reads (pre-processed). So that is around 200 GB of data in total.
The problem is that I would like to do mapping on my PC since uploading to a server such as Galaxy would take too long (internet is slow where I live).
My computer has a 16 GB of RAM and AMD Ryzen 5 1500X Quad-Core processor. I am trying to map to a reference genome ~500MB, 3300000000 bps, N50=30000.
The mappers that I considered are STAR, BBmap and GMAP/GSNAP. From what I have read GMAP/GSNAP is the fastest and is not so memory hungry, but BBmap and STAR are also praised on forums. Which one would be most appropriate for me? Is it even possible to run them on one of my samples with my PC? And which mapper you have the "best experience with"?
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bbmap, cpu requirement, gmap, ram, star aligner

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