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Hello All,
Suppose I have 80 samples from different mutants of Arabidopsis thaliana, 30 million reads of 50bp each sample, sequenced by Illumina , two flow cells, what kind of equipment (machine? computer?) do you think I can use to analyze the data in a reasonable time, and how much it will cost?
By the way, do you think TopHat is good for aligning 50bp reads? Is there other alternatives for short reads? I am asking this because TopHat is optimized for reads of 75bp or longer.
Thank you in advance for your kind reply.
Suppose I have 80 samples from different mutants of Arabidopsis thaliana, 30 million reads of 50bp each sample, sequenced by Illumina , two flow cells, what kind of equipment (machine? computer?) do you think I can use to analyze the data in a reasonable time, and how much it will cost?
By the way, do you think TopHat is good for aligning 50bp reads? Is there other alternatives for short reads? I am asking this because TopHat is optimized for reads of 75bp or longer.
Thank you in advance for your kind reply.