Hi!
I have some questions about optimising the speed when using TopHat2 for mRNA analysis.
As a testrun I used this command:
tophat hg19 /path/to/x.fastq
hg19 was manually indexes using Bowtie2.
Here you see the Activity Monitor during the run:


So, my questions:
1. Is it normal to use so little of the total capacity?
2. I have downloaded the iGenome hg19 as well as the not pre-built, the BT2 index files are not the same size as the ones I made myself, should I switch to using the pre-buildt hg19?
3. What is the "AbundantSequences" included in the pre-built hg19 and how can I use it in my mRNA analysis?
4. Is there something else I should note when working with mRNA analysis, like exclude all introns in hg19, or something?
Thank you very much!!
I have some questions about optimising the speed when using TopHat2 for mRNA analysis.
As a testrun I used this command:
tophat hg19 /path/to/x.fastq
hg19 was manually indexes using Bowtie2.
Here you see the Activity Monitor during the run:
So, my questions:
1. Is it normal to use so little of the total capacity?
2. I have downloaded the iGenome hg19 as well as the not pre-built, the BT2 index files are not the same size as the ones I made myself, should I switch to using the pre-buildt hg19?
3. What is the "AbundantSequences" included in the pre-built hg19 and how can I use it in my mRNA analysis?
4. Is there something else I should note when working with mRNA analysis, like exclude all introns in hg19, or something?
Thank you very much!!
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