reduce the number of simulated clipped reads

[jazberna1]

Hello,

I was wondering if there is a way to control how many clipped reads are simulated via Varsim (or Art).

Many thanks
Jorge

[yunfeiguo]

Hi @jazberna1 what do you mean by clipped reads here?

[jazberna1]

Hello Yunfei,

Yes, let me explain. I have used varsim to simulate 1000 insertions in the human reference genome, and the generate PE illumina reads based on that artificial genome. What happens it that when I map those reads back to the original human reference genome I see a a high amount of clipped reads, much more than I had expected all over the genome, regardless of the extra clipped reads due to the simulated inversions.

Thanks
Jorge

[yunfeiguo]

Is it possible to simulate 1 insertion or invesion and check if the results are consistent with expectation? If it's not working, you can send me the command to reproduce this issue.

[jazberna1]

Hi Yunfei,

I'm repeating the simulations passing --art_options="--errfree" and see if that has to do with the excess of clipped reads.

Jorge