Question about Tophat2-parameter"-r <int> 50 as default"and "--mate-std-dev <int> 20 as default"

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7.9 years ago

Yunlong JIA ▴ 40

I ran my data using Tophat2, for the "-r" and "--mate-std-dev", I left them as default value.

Next, I watch the paired-end reads in Savant Genome Browser, I check the insetsize for the paired reads, they are so variant.

As default, insersize should in the range of 50(+- 20), from 30~70. But I found many insersize bigger than 200nt, or overlapping.

Why the default value didn't work? The default is randomized insertsize when pairing the reads?

Hope your help, thanks.

RNA-Seq Tophat2 parameter • 1.5k views

ADD COMMENT • link 7.9 years ago by Yunlong JIA ▴ 40

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I just asked a different poster to do this and will ask you as well.

You can use BBMap (if your reads don't overlap) or BBMerge (if you know that R1/R2 overlap) to get an idea of insert size distribution. Both programs are part of BBMap suite. You will want to use ihist= flag to create a file with insert size distribution.

ADD REPLY • link 7.9 years ago by GenoMax 141k

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Thank you, maybe it's some bug for tools, thanks for your advise, I will try this BB.~

ADD REPLY • link 7.9 years ago by Yunlong JIA ▴ 40

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