Question: How To Do Quality Trimming Of Solid Reads In Colour Space?
5
gravatar for Allen Yu
9.3 years ago by
Allen Yu200
Allen Yu200 wrote:

The reads returned from the Solid sequencing provider are littered with dots and some bases have a negative quality value. Does anyone know if there is a good method to extract high quality regions from the reads without distorting the reading of bases in colour space?

solid • 4.1k views
ADD COMMENTlink modified 13 months ago by sysabayaseenbutt0 • written 9.3 years ago by Allen Yu200
4
gravatar for Curious George
9.3 years ago by
Curious George40 wrote:

The Solid Accuracy Enhancer Tool might be useful for this.

edit: original link was pointing to a malware site.

ADD COMMENTlink modified 13 months ago by h.mon25k • written 9.3 years ago by Curious George40
1

Thanks a lot for your kind help, the number of dots in csfasta reads does become lower.

ADD REPLYlink written 9.2 years ago by Allen Yu200
4
gravatar for Mikael Huss
9.2 years ago by
Mikael Huss4.6k
Stockholm
Mikael Huss4.6k wrote:

I know of two quality filtering methods for SOLiD reads, besides the already suggested SAET:

Haven't actually tried any of them yet, but will do so pretty soon.

edit: original link to the csfastaqualityfilter.pl was pointing to a malware site.

ADD COMMENTlink modified 13 months ago by h.mon25k • written 9.2 years ago by Mikael Huss4.6k
0
gravatar for Antonio R. Franco
4.7 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

It seems that the Dr. Michael's tool are not longer available, neither the csfastaqualityfilter.pl

Can anyboy either send me these tools/scripts to me or indicate where to get them? My address is arfranco (at) uco.es

ADD COMMENTlink written 4.7 years ago by Antonio R. Franco4.0k
1

There are some tools still available on our site, see if SAET would work for you:

Solid Software Tools: Denovo Assembly/Xsq Tools Pipeline Mirrored At Biostar

ADD REPLYlink written 4.7 years ago by Istvan Albert ♦♦ 80k
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