How To Visualize The Quality Of Sequencing Data In Colorspace (Solid) Format?

Question

[Roger]

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

[Leandro Lima]

Hi Roger. Have you tried LifeScope?

[gauravdube007]

Hello Leandro Lima can you please help me with this post?

Thanks in advance.

[Ashutosh Pandey]

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?

Answer 1

[Istvan Albert]

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

[Roger]

10ks Istvan. You're the MAN.