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How To Set Shrimp Parameters For Best Sensitivity With 35Bp Colorspace Data?

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!

short aligner sequencing
• 4,079 views • link
updated by Ram Ram • written by Zhaorong Zhaorong

2 answers

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.

• 9 views • link
written by Gue Su • Gue Su

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.

• 15 views • link
written by Istvan Albert Istvan Albert

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