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How To Visualize The Quality Of Sequencing Data In Colorspace (Solid) Format?
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6.1 years ago
Roger • 0

Hi all,

I've a colorspace library. Everybody knows that SOLiD has low-quality ends from reads. So, I would like to know if there are one tool to check this quality graphically. Just like a dotplot of my reads quality.

For example:

csfasta 33231223214523

qual 29 32 29 9 4 6 -1

And the graphics will be:


| G | G | G | W | W | B |


G = Good W = Warning B = Bad

Any help will be greatly appreciated.

10ks

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Hi Roger. Have you tried LifeScope?

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What exactly you are looking for? There are many solid based read-trimmers that you can search here on biostars. What purpose visualizing the quality of read will serve?

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8 weeks ago
University Park, USA

Transform the reads to either color space fastq via double encoding or just decode it to FASTQ and run a FASTQ based quality control tool on it: fastqc etc.

There are some tools mentioned here: Transforming and manipulating color space reads

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10ks Istvan. You're the MAN.

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