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reduce the number of simulated clipped reads
Hello,
I was wondering if there is a way to control how many clipped reads are simulated via Varsim (or Art).
Many thanks Jorge
Hi @jazberna1 what do you mean by clipped reads
here?
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
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.
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