soap 2.18 problem

[Xiaomin Ying]

Hi,

When I mapped short reads to human genome using soap 2.18, lots of errors of "length y < 0, countinue as 13" occurred and a fatal error of "Segmentation fault" occurred in the end. What's the problem?

Thank you in advance.

Best,
Xiaomin

[chang yu]

Hi Xiaomin,

Is there many reads shorter than 30bp?

This will cause theSegment fault.

Chang

[Xiaomin Ying]

Yes. I also found it. Anyway, thank you very much!

Xiaomin

2009/7/13 chang yu <ychan...@gmail.com>

[Spade]

Hi Chang,

So, does SOAP not support reads shorter than 30 bp. In my
case, I have SBS reads which are initially 40+ bp long, but separation
of a 5 prime adapter from these reads leaves me with reads that range
from 18 bp to 37 bp length. Does SOAP offer a solution for matching
these to large genomic files at the promised speed? I'd appreciate
your response a lot.

Thanks,
Spade

On Jul 13, 2:48 am, chang yu <ychang0...@gmail.com> wrote:
> Hi Xiaomin,
>
> Is there many reads shorter than 30bp?
>
> This will cause theSegment fault.
>
> Chang
>

[chang yu]

Hi Spade,

Actually, current version SOAP could support shorter reads, but it will be lost some case when there are 2 or more mismatches, so we do not recommend to do this.

Chang

[Spade]

Thank you Chang for replying.
- Spade

On Jul 21, 6:34 pm, chang yu <ychang0...@gmail.com> wrote:
> Hi Spade,
>
> Actually, current version SOAP could support shorter reads, but it will be
> lost some case when there are 2 or more mismatches, so we do not recommend
> to do this.
>
> Chang
>