Help about setting up TopHat

[lewewoo]

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!

[Jon_Keats]

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
(http://seqanswers.com/forums/showthr...?t=4589&page=4)

[lewewoo]

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

thanks!

(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)