Question: How To Set Shrimp Parameters For Best Sensitivity With 35Bp Colorspace Data?
1
gravatar for Zhaorong
10.9 years ago by
Zhaorong30
State College, PA
Zhaorong30 wrote:

Hi,

I have 35bp Solid colorspace sequencing data, and the actual sequences to be mapped are 20-25bp after removing the linker sequence.

I hope to find all the hits allowing no more than n mismatches (say n=3), not only the best hit.

I know there is a -M option to specify -M sensitivity,35bp. I wonder whether this setting will guarantee the best sensitivity in this case. Since my reads are only 20-25bp long, should I changed the default 4 spaced seeds to 3?

I'm new to SHRiMP, so I'd like to hear some suggestions on setting the parameters of SHRiMP to achieve the best sensitivity.

Thank you!

shrimp sequencing short aligner • 989 views
ADD COMMENTlink written 10.9 years ago by Zhaorong30
2
gravatar for Gue Su
10.9 years ago by
Gue Su20
Gue Su20 wrote:

I just read the SHRiMP manual again, but I think that their explanation about -M option may not be enough to answer your question. I usually use the "seed" mode by using -s, -n, and -w and the option -M is a new feature of the version 1.3.1, which I have never tried before.

I recommend for you to use the "seed" mode--the default would be good, but please adjust the -s option if you want more sensitivity. Always fast speed compensates sensitivity and the -M option seems to exist for this purpose.

Hope my message to be helpful for your project.

ADD COMMENTlink written 10.9 years ago by Gue Su20
1
gravatar for István Albert
10.9 years ago by
István Albert ♦♦ 310
University Park
István Albert ♦♦ 310 wrote:

Since my reads are only 20-25bp long, should I changed the default 4 spaced seeds to 3?

while the shrimp manual says:

  • We recommend using the default 4 seeds of weight 12 in most cases.

you could try running on a smaller sample and see what happens.

ADD COMMENTlink written 10.9 years ago by István Albert ♦♦ 310
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