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Old 11-14-2011, 03:36 PM   #1
Location: Moon

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Default Help about setting up TopHat

The sequencing people in house told us that the library fragments range from 200-500 bp with a major band at ~280bp, so for tophat setting, how could we set up -r? we have 100 cycles for read1 and 100 cycles for read2.

tophat -r 80 index/index_mm9 R1.fastq R2.fastq


(previously, the sequencing results from Illumina just informed us 75bp for paired end reads, and total fragments are 300bp, so we set up -r as 150)

Last edited by lewewoo; 11-14-2011 at 03:38 PM.
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Old 11-14-2011, 04:57 PM   #2
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Perfectly correct way to do it. If you want to do it based on the actual read data, align a subset 1-5 million reads to a transcriptome reference with bowtie or bwa, run picard insert metrics to get the true mean, median, standard deviation of each library.

There is code for this on my introduction thread
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Old 11-14-2011, 06:52 PM   #3
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Thanks a lot!
Tophat said "-r" is an expected number, that means Tophat just requires a "-r" number to estimate the mean number and your script could do a better measurement for the mean, right?
Thanks for sharing!
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